My friend who works for a computer store recently rescued a 486 from the recycle pile. We immediately turned it into a dos gaming box, but an issue with the gameport has occurred.

Specs
486DX 50mhz (50 mhz bus speed)
8mb of ram in 30-pin simms
VESA 1mb Diamond Speed Star pro graphics
Windows Sound System
16-bit ISA IDE interface
8-bit ISA Paralell/Serial/Gameport interface (gameport can be disabled via a jumper)
8-bit ISA Dual Gameport card(added by us)

We installed Windows 95, and then ran several games in dos mode using a gamepad. The games seemed to work okay with a gamepad at this point with the original gameport. Needing a second game port, we ordered the ISA card and installed it, disabling the original port via the previously mentioned jumper. We also installed direct X 6 into windows, and then software for a Microsoft Sidewinder 3d. Using the windows gamepad control panel we calibrated and used a gamepad to play a game of Stargunner, which worked perfectly.(also stargunner has built in calibration)

We then ran one of our previous games, in this case Golden Axe, and the gamepad now skews up and left, no matter which gameport is in charge (or installed), in or outside of dos mode.
This calls into question whether it was working well previously or not.

At this point we would like any suggestions for fixing it.

Previous attempts:
Trying different gameport cards, and gameports.
Adjusting the bus speed in the bios to 1/10th of the clock speed
Different ISA slots for the gameport cards.

Any and all suggestions will be helpful, Thanks in advance!