The 0.0.1 is by design (as part of the modloader). The idea behind this is to prevent someone with a mod from accidentally joining a non modded game and having all sorts of problems (game desynch basically, for example, if a mod used a modified sheets or something that would cause problems). Instead of experiencing problems with the game desynching / crashing, the host will simply eject the player (because their version number is wrong).
There is an exported function from op2ext.dll, SetSerialNumber() that lets you set the version number to whatever you want. (So that all mods don't have to use 0.0.1 and thus risk conflicting with each other). It takes 3 chars as parameters and I believe it uses __cdecl calling convention.
Arklon, you could probably do something like the following to get it to work:
// Inside of mod_run in your op2mod.dll
HMODULE hmod = (HMODULE) GetModuleHandle("op2ext.dll");
void (__cdecl *SetSerialNumber)(char c1, char c2, char c3) = (void (__cdecl *)(char,char,char)) GetProcAddress(hmod, "SetSerialNumber");
SetSerialNumber(1,3,4);
to set it back to 1.3.4 for compatibility with the original game. If it crashes, change __cdecl to __stdcall.
If you're willing to wait for a while (probably a day or so), I can give you more elegant code that doesn't require nasty casting tricks like the above (obtain a function pointer and call it). (basically a header file and import library. I don't have those on my computer right now).