As you've probably realised, recording in Multitrack and Waveform views are considerably different. Multitrack records direct to disk, which is a much better, safer way to record. Waveform view, on the other hand, records via a temporary file, and your finished result isn't written to your final file until after you've finished recording. It's the way that Cool Edit Pro (Audition's predecessor) originally recorded, and it allows you to run 'undos' by nesting the temp files; every time you change something in a file in Waveform view, a new temp file is created. If you are editing a one hour file, these temp files get to take up a lot of space. By default, Audition uses the same temp space as the OS, and this is simply an appalling idea.
So even though it might not be the actual cause of your problem (although it could be), it's a good idea to relocate Audition's primary temp space to somewhere where the OS (which does weird things with the temp space allocation) isn't going to attempt to over-ride what's happening in the folder. Ideally, have a separate drive for temp files. On the DAW I use a SSD for this, and regard it as sacrificial - even though it hasn't actually ever crashed.
But the thing that makes me a bit more suspicious is the moving levels with silence, etc. This sounds more like a corrupted driver than anything else. You haven't said what sound device you are using, but have you checked to see if there's an updated driver for it? The other driver that would also alter the way things are displayed is the video driver, and in many ways, that's where I'd look first, as these are well-known for causing all sorts of problems.
That should be enough for the time being!
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