Do you know which shift key is causing the problem? You can disable shift keys in X using xmodmap. For example, to clear all shift modifiers:
xmodmap -e "clear Shift"
To add back the left shift key to see if itís the problem:
xmodmap -e "add Shift Shift_L"
To add back the right shift key to see if itís the problem:
xmodmap -e "add Shift Shift_R"
You will obviously need to use Capslock to capitalize the appropriate letters (e.g., in ďShift_L
If both keys are bad, you might turn your Caps Lock into a Shift (instead of a Lock).
Note that the above might not carry over into libraries which make use of low-level keyboard events (e.g., SDL). In order to eradicate the troublesome key completely, you will need to make the change at the kernel level.