I'm assuming you want to do something like record game Audio/Video with real time voice chat through something like Ventrilo or TeamSpeak, correct? If this is the case, I can see the need for both to be recorded in real time. Unfortunately, however, it also tends to be very difficult to do without either two sound cards or one professional card with multiple inputs.
In your case, the simplest solution would likely be to buy a headset you can plug in via USB. The USB connector, at least on some of the higher end ones, will act as a second sound card and you should be able to feed it's input and output to separate tracks in an audio recorder.
Here's something else you could try if you don't want to buy a new headest. Get a 1/8 inch line cable and a splitter. You would need a male input split into one male and one female output - this may be hard to find. I'd look for you but I'm a bit short on time at the moment. Run the cable from your headphone jack into your splitter. Connect one end of the splitter to your mic input and the other to your headset or mic (assuming it is also 1/8 inch). Now, your mic will be getting audio from two sources at once and should be able to record on a single track. Then, just disable the audio track from Fraps and you should be good to go. The only concern here is volume balancing which would have to be done individually on the two sources before you started recording.
There is one other thing you could check though and that's your Fraps settings. I haven't used the program myself but make sure it's not doing anything to speed up or slow down your game's audio or video. That could be a source of your timing issues.