So when I play Cortex Command, my mouse doesn't always respond. Sometimes when I click, my guy will shoot, sometimes he won't. It makes it really hard to play, as you can imagine.

If you have any input into this situation, please help me.

Is the issue happening with other programs?
Can you click, hold, and drag Windows around without it dropping them unexpectedly?
Check these first and try reinstalling CC and/or reinstalling/updating the drivers for your mouse if the above tests prove alright.

No it's just with CC. I tried reinstalling the program too, but with the same results.

And your drivers are current?
Run the windows self diagnostic on your mouse too for kicks.