Recording in Multitrack goes direct to the final file. Recording in Waveform view goes to a temp file first before it's saved. By default, this temp file is in a common temp file area that the OS can also use, and it has priority. Ideally you should relocate your Audition Primary temp file space to a drive of its own, but if you can't do that then at least give it a folder of its own.
Edit>Preferences>Media and Disk Cache. Don't worry about the Secondary temp - on most systems you don't appear to need one.
Also, it sounds as though your sound device latency setting might only just be on the brink of 'okay'. You could also try increasing it one step.
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