Hang in there~! It will take a couple of weeks for Bear's body to get used to the Pheno'. Yes, the hind end problems could be a side effect of it, and, it can also be residual effects of his seizures. It took Woody a few weeks to get settled into the Pheno' when he started (around 8 or 9 years ago now). Oh, and Bear is probably not feeling too great as his body adjusts. Plus, the Vet's need to find the correct amount of Pheno' for Bear, and even knowing his weight, this may take time as his body adjusts. You don't say if Bear takes one dose a day, or two, but, I found with Woody, 2 doses at a lower level work much better than one. It seemed that the 1 wore off in the evenings. The pee'ing thing will get better, but, you will find he drinks excessive amounts of water (therefore will have more output) as a permanent side effect of the meds. For me, this side effect was much better than watching Woody have Gran-mal seizures.
As far as causes for the seizures, there may be no identifiable ones to find. My vet told me that this is the case in many male dogs between 2-6 who start having seizures. I had all the neuro tests done with Woody, and the results were just that I had A LOT less $$$ in the bank. We never figured out what the causes of his seizures were.
Good luck with Bear, it's hard to see, but, with regular doses of Pheno', it should get better in a few weeks :-)
Sorry, this got a bit long~!