Did you use a 32-bit version by any chance? That would explain the 3GB limit.
I was guessing the same thing but wanted to make sure exactly what was causing the crash first (if the super large wallet is causing blockchain corruption then perhaps that is a bug that should be reported).
OP should note that if they are using Windows then they are using a 32 bit version (so a possible fix might be to change to a 64 bit Linux version).