For some reason whenever using Mechjeb, it closes all my solar panels when warping for longer amounts of time. It only happens when using Mechjeb and I've tested it on about 10 different designs. I also tried it on stock with only Mechjeb installed and the same thing happens. My output log doesn't give any hints on anything messing up either.

I can warp for 100+ years inside Kerbin SOI but the second Mechjeb warps outside the system it automatically closes all solar panels! It doesn't make any sense to me

yes this is strange mainly because Im pretty sure MJ doesn't have the ability to close or open panels. make sure there isnt anything else installed that can do that, maby its a conflict in the codes of two mods.

MJ has the ability to open/close solar panels in the latest builds

no, this is totally unrelated.