Uh oh im sorry it was my fault, not the emulator.
I coded a little routine that changes the RAM page to 01 (#04 written to $5113), write some bytes, then read the first one. If it did not match, then my game would return an error message as follows:http://www.a3share.com/members/1119/ramtest.PNG
If it did match, then the rom would load normally. After that $5113 is set back to #00.
until I discovered that this was all because I never actually wrote to $5113 in the RESET code, so that's why. So I added a 00 write to 5113 in it, and then now nestopia loads my game properly now with no problems.
Sorry about that. My mistake.