Sometimes slow hard drive access times can cause stuttering in recording or playback. If increasing the buffer or latency settings in the sound device preferences (File Menu > Preferences > Sound Device) doesn't help, and you have Mixcraft 5 or higher, try this:
1) In Mixcraft, click on the File menu and select Preferences.
2) Choose the Recording preferences.
3) Try switching the Recording File Type setting from "Uncompressed Wave File" to "Compressed Ogg Vorbis File."
4) Now record something and see if the problem is gone.