Jacked up controls

Ok. The emulation and graphics part works perfectly fine for me. Great emulator. However, I seem to have a small control issue. About three minutes into a rom, (Say Mario 64 from the beginning to about the time you reach the huge Chain Chomp) the directional functions of the emulator will stop responding. I'll be holding a direction, and when I release it, Mario will continue moving. The buttons will still work, but the control stick will not. (Mario can still jump, dive, camera controls still work, etc.) Exept with about a 1 second delay. After mashing keys for 5 minutes, I will regain control, then lose control again, this time without ever regaining it. Then, when I exit TR64, the keyboard all but ceases to function. (I'll mash like 20 keys and one will be detected.) I tried switching to a previous version of TR64 and that doesn't seem to work. In fact, it seems to make it worse. Could this be the control plugin's fault? Is anyone else experiencing the same problem?

EDIT: Dude, it's been like 2 weeks, and no one has replied. I figured out a way around the problem, but not through it (Yes, there is a difference). I can have a text-editing program open such as Notepad during play, and when this happens, I switch to the document and press a key twice. The first time it is pressed, nothing happens. The second time, the key is printed to the screen. Meanwhile, Mario is running off a cliff or Fox Mc. Cloud is busy flying into walls. Anyone see what I'm doing wrong? I tried changing the directional buttons to actual character keys, but that didn't help. Someone? Anyone?