I have read several reports where homemade PFA has been cited as the cause of unreliable polymerisation of the hydrogels. I have also had some problems with homemade PFA that seem to be resolved by ensuring the pH of the PFA is >7. I believe that a low pH could inhibit the thermal initiator but I am not sure. Could this be the case? Or could excess protonation inhibit cross-linking directly?
I have made 4 large batches of the Hydrogel solution, used it fresh and thawed, and always get a good hydrogel.
Most important is to make sure you have no oxygen touching the hydrogel when you are polymerizing. I either fill up the tube all the way with solution, or I use "Private Preserve" a mixture of heavy gasses that I use to preserve my red wine after I have opened a bottle