I had a similar problem some years ago.
I could see a "warble" on my PSK31 signal on the waterfall of my digital
modes program MixW. It only happened on certain bands which, in
retrospect, was the giveaway. I rebuilt the PTO a number of times and it
didn't fix the problem so I put the problem on this reflector. The cause
was spotted - after much discussion of red herrings - by a K1 who said
it was the offset voltage pot on the control board. It had a dirty track
and a squirt of switch cleaner did the trick.
Eventually I replaced the pot.
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