Hi, I'm Dr. Bonk. I'm very sorry to hear about Rudolf's troubles. Epilepsy is a tough one to control and sometimes drug dosages have to be changed multiple times within a dog's life. I'm sorry this has been so tough and Rudolf and you.
Epileptic seizures can be triggered by numerous, sometimes unknown, causes even while on medication. Also, phenobarbitol can take several weeks to reach treatment levels. This means each time the dosage is changed, it can take two weeks to adjust. Some dogs, benefit from the addition of another antiseizure drug called potassium bromide. Potassium bromide works together with phenobarbitol to control seizures. Again, potassium bromide can take a couple months to reach treatment levels, so there is a period while starting the medication when you will see little to no improvement.
Usually what benefits these dogs during this adjustment period is Diazepam given per rectum during seizures. Diazepam is a muscle relaxant, so while it doesn't really stop the seizure, it makes it less traumatic on the dog's body so that recovery is quicker and easier. Most vets will dispense some for you to have on hand.
Finally, the muscle weakness can be brought on by the seizures themselves. Seizing takes a toll on the body. It would be like running a marathon when you haven't been training for it, especially if multiple seizures happen in a short period. Phenobarbitol can also cause some lethargy at the initiation of treatment and with any dosage changes. You can try giving him an antiinflammatory such as Rimadyl or Previcox to help with any muscle soreness.
If the seizures don't decrease after a couple of weeks on the increased dose of phenobarbitol, consider adding another antiseizure medication such as potassium bromide, and see if your vet will dispense Diazepam for you to give during seizure episodes to lessen the affects for Rudolf.
I hope this helps. Please contact me with any further questions you may have. Thank you and good luck!