I have the same guitar with different knobs but with the same problem. I bought it used and was unsure if was aftermarket pots or knobs. To fix it i originally filed the top of top post down a little, but that didn't really work so I drilled out the base of the knob a little and it sat down nicely. I'll grab a pic in a few days as the guitar is at my practice studio and I won't be there until Tuesday. Interesting to see someone else had the issue.
That's interesting, but it sounds to me as if your pots where sitting uneven. In my case the pots are even, but the knobs are different.