[TippeX]

probably just a crc check, its relatively hard in a high level language to force code cave generation in the code (especially if you have the compiler optimisation flags) so i'd say its pretty rare

unaltered exe file? well how would it be a patch/upgrade?

change in opcode can be one of 2 possibilities

1. crc used
2. actual opcodes are used as a crypt/decrypt key

you just need to investigate it further, remember that its very rare for this sort of stuff to be put in at compile time, rather its done after compile, via binary patching / external tools and so on, so at one point in time the code was 'clean', thus, if the stuff is removed properly, the code should run fine.