There are a few things that could cause this.
1. "Stuttering" could be caused by other programs running in the background. On fast processors, this is not likely to be an issue, but on slower processors (say, 1.5 GHz or less?), it may be an issue. If the stuttering always occurs in exactly the same place, then the problem occurred during encoding, and you will need to re-record the track. If the stuttering does not occur in exactly the same place, then the problem is occurring on playback and the file is probably fine.
2. "Popping" or "Clicking" is most likely caused by either: driver problems or clipping. Driver problems are tough to troubleshoot, but if you just installed new software/hardware, that might point to driver problems as the cause. Try changing MC from "Wave Out" to "DirectSound" and see if that resolves the issue. If so, it may be driver problems. Clipping occurs when the sound level goes too high (loud) for the file to hold it. Part of the wave form is lost and the result is a pop, click, or in very bad cases, maybe even a buzz. If clipping is the problem, the pop/click will always be in the same place in the file, and it will tend to occur at loud parts of the track (e.g. when the bass drum hits or when the singer hits a loud note). You can avoid clipping by turning down the input level either in your recording program or in Windows mixer. You want as loud a level as possible (in order to maximize signal and minimize "hiss"), but not so loud that it clips. In any case, if clipping is your problem, you will need to re-record the track.