That is an odd one...

- What happens if you use 512x TC instead? How about 128x?? Does it do it every time in 256x TC? When you activated the mod, did you empty your Save folder, generally in "C:\Users \UserName \Documents \SH4" or similar, OS dependent? Do you use the LAA applet to set the bits on the SH4.exe file, to where Windows "knows" that SH4 is capable of addressing more than 4gig of RAM? Thanks.
In the meantime, nothing to be "sorry" for in this. It's just a game, and is rather recalcitrant in its relationship with us mere humans...