Even your best lipo can only be used some many times, and some uses will cost you more than others (like 4wd SC vs stock buggy are night and day different in demand on the battery).

Running paired setups like that do not mix old and new batteries, they need to be pretty close in age/use and the same specs. Otherwise you run the risk of getting something below a safe voltage at the very least.

My guess is the old batteries are just tired and in need of replacement.