Well, anything is possible.
It might be helpful if you indicated exactly what controller you are using. Perhaps someone who owns one like it will be able to give some information about problematic games or circumstances.
One thing that might be worth checking is what resources your motherboard is currently using for the gameport. Even if the game documentation doesn't list them specifically, the game may be looking for particular values to be used for a given resource type. For example, I have played the game on one machine of mine that has a Creative Sound Blaster Live! (CT4760) that is set to use the following resources in the SB16 Emulation:
SB Port: 220
MPU 401 Port: 330
ADLIB Port: 388
IRQ: 5
8-bit DMA: 1
16-bit DMA: 5
These are fairly "safe" values that are acceptable in most DOS games.
Edit: I left out the most important value (sorry):
Gameport I/O: 0200-0207