my audio has a bunch of skips and jumps in it

Yes, I was afraid it might be. Waveform records to a temp file, and the save of your actual file doesn't happen until you've finished recording. The trouble with this is that Audition's temp file generally shares the same space as the OS one, and this has all sorts of ramifications; essentially what you've got is temp file corruption. The first thing to do is to relocate Audition's temp file to a directory of its own - but make sure there's enough space, because this also has to store all the 'undo' files for editing. You can alter the amount of those that are saved in Preferences, and it's generally a good idea to limit that to a smallish number, especially if it's large files you are editing (not such a problem with short ones).

The best solution though is to record in Multitrack view. This writes your files direct to disc and doesn't go through all the rigmorale and crash potential that Waveform does when recording. It's generally a much more stable way to record, and even if your computer crashes, you stand a good chance of the file you're recording still being available for recovery afterwards. That's always a very dicey proposition with Waveform recording...