Gas side of fridge works perfect all day, stops during night!

I have a 1994 RV with a Dometic RM7030 side by side. It has AES and really works great when transferring. I mostly run on gas because of no shore power, but I do have a generator. It works flawlessly on electric and for the most part on gas too. Awhile back, I had trouble lighting on gas and there was a pile of rust built up under burner/ thermocouple area, so I cleaned out the rust and everything seemed normal again. Now during the wee hours(3-5 a.m.) it shuts down. It relights usually without too much trouble,1-2 tries. Could the thermocouple be the culprit or is the rust(wherever it's coming from) part of the problem? Is this rust normal? I'm thinking rust can't be good. Thanks for any help you can give me!