The reason I linked the full study was to provide the proper context of it. It's important to note that it was not linking seizures/epilepsy to being vaccinated, but indicating that

Early diagnosis of the corresponding epilepsy syndromes and confirmation of an underlying etiology is important for treatment decisions, genetic counseling, and public health evaluation of vaccine safety.

And it's also important to note these stats:

In total, 328 cases of suspected vaccination-related seizures and epilepsies reported between 2006 and 2008 were analyzed (2006, 101 cases; 2007, 102 cases; 2008, 125 cases).

Fifty-one (15.5%) of 328 patients presented with nonepileptic events....
For 37 (11.3%) of 328 cases clinical characterization was difficult due to incomplete information.

Of the 328 cases, 26.8% were either non-epileptic and showed no seizures or weren't able to be classified.

Also, to be noted...

The number and relative frequency given for seizure types and epilepsy syndromes are reported as a percentage of the total number of epileptic events, as the denominator of the total number of vaccinated subjects was not known.

The stats presented are only in relation to reported cases in this study. The percentages of epilepsy/seizures is not a percentage of the total number of people vaccinated. These figures are only taken from the small subset of individuals from the three-year period of 2006-2008.

And then there is this...

Clinical characterization of all cases with data supportive of seizures or epilepsy reported between 2006 and 2008 revealed 11.7% of cases presenting with severe epilepsies of infancy, including four patients (1.6%) with confirmed Dravet syndrome who had mutations in SCN1A. Because the clinical information provided was strongly suggestive of Dravet syndrome in an additional four cases (1.6%) and genetic factors are increasingly identified in patients with West syndrome (Watanabe, 1998), we suggest that causal genetic factors could potentially be identified in a sizeable subset of patients with severe childhood epilepsies and vaccination-associated seizures, helping to further demystify the concept of “vaccine encephalopathy.” As discussed by Berkovic and colleagues (Berkovic et al., 2006; Mcintosh et al., 2010), identification of a mutation in SCN1A or other epilepsy-related genes does not rule out the vaccination being a trigger for onset of seizures. However, given that truncation or missense mutations in conserved regions of the SCN1A gene have not been found in healthy control subjects, children carrying the mutation would seem destined to develop the epilepsy syndrome irrespective of immunization.

In other words - the vaccines aren't necessarily the cause of the seizures/epilepsy in many cases, but they may trigger them due to an existing genetic condition/disorder. Identifying and understanding these genetic dispositions would help doctors and parents with the decision-making process for their patients/children.

And these comments don't really support the anti-vaccine claims...

Our results suggest that close follow-up of patients with vaccination-associated seizures around the age of 6 months and further seizures or additional symptoms such as developmental slowing could help to identify cases of Dravet syndrome early in its clinical course, allowing for timely medical intervention to prevent further seizures. Importantly, cases of Dravet syndrome can masquerade as so-called “vaccine encephalopathy.” Elucidating the genetic basis in these cases will establish the diagnosis, avoid further diagnostic procedures, allow for genetic counseling of the family, and finally might remove feelings of guilt in parents.

A recent study of the impact of vaccination on seizure onset in Dravet syndrome did not find any differences in the course of the epilepsy or cognitive outcome between patients with onset following vaccination compared with patients whose onset was not related to vaccination. There was also no observed effect on outcome when additional vaccines were administered after seizure onset (Mcintosh et al., 2010).

Because infantile spasms typically start at around 6 months of age, onset of seizures might coincide with routine vaccination. A possible causal relationship between vaccination and West syndrome remains controversial (Bellman et al., 1983; Goodman et al., 1998; Guggenheim et al., 2008).
West syndrome requires particular attention with respect to the diagnosis of possible underlying etiologies such as genetic causes (Deprez et al., 2009) or cortical malformations (Guerrini & Marini, 2006) and an assumption that a proximate vaccination is causative should not be made.

However, passive surveillance systems have several limitations (Singleton et al., 1999; Varricchio et al., 2004), including underreporting (Hasford et al., 2002), lack of exact exposure data, reporter bias, and variability in the quality and completeness of information provided. Whereas events with low impact on the health of a child might be lost to underreporting (Rosenthal & Chen, 1995); patients and parents who oppose vaccination programs may overestimate possible relationships between diseases and vaccination, thereby creating a reporter bias. Furthermore, severe events occurring in young children appear to be more likely to be reported (Hasford et al., 2002).

Results obtained from passive surveillance are not suitable for determining the frequency of a particular adverse effect. With respect to our study, we are, therefore, unable to generate incidences or relative risks of certain epilepsy syndromes in relationship to vaccination. However, given the high coverage for recommended childhood vaccinations (Reiter & Poethko-Muller, 2009), the frequency is likely to be very low.

The data that they present doesn't conclude with "vaccinations do cause seizures and epilepsy," but instead it essentially states that seizures/epilepsy often occur around the time of vaccination due to genetic conditions/mutations and the fact that the vaccination timing coincides with when many of these symptoms begin to present themselves in childhood.

That being said - fever is one of the side-effects of vaccinations and severe fevers can cause seizures (febrile seizures), so there's always that risk involved. And the febrile seizures were over 55% of all of the reported seizures in this study. But it should be noted that febrile seizures can occur from any rapid increase in body temperature, so the causes are in no way limited to vaccinations. Futhermore, something like 35-40% of children who experience these seizures will likely have additional seizures throughout their lifetime.

While most of these seizures occur in children and around the time of vaccination, the continued seizures aren't really a result of the vaccination per se, but often a result of an associated fever due to receiving the vaccination.

So, it's not the pharmaceutical companies "poisoning" or trying to kill your children by putting bad things in the vaccines. The vaccines work. The problem is that some children just shouldn't receive them and other relatively small numbers of children unfortunately have a bad reaction, resulting in a fever and consequent seizures. In any case, all of this should be openly discussed with your doctor beforehand and I think that's where most of the failures occur.