So, brought both keys to a shop and they tested the keys as working fine. I opened them up, changed one battery with a new one and checked to make sure the contacts are clean and making contact. Problem still persists. My wife's theory is that something happened when the battery was drained one night because she's certain it's been happening since then. I brought the battery to the company I brought it from and they tested it as fine.
They said it was at 89% charge and it seemed a little low. Put the battery back in and checked the charging voltage at the battery terminals. it was reading between 13.8 and 13.9. My van with a new alternator and 2 yr old battery charges at 14.3v.
Doesn't seem too far off but it is off enough that it could be making the car unhappy? should I be looking into replacing the alternator? any other ideas?