In your user's manual, it specifies connecting the analog source (your turntable/phonostage) to the CDR/TAPE/MD input. I don't see any AUX input on your receiver, so use the IN RCAs of that input. (Edit: was typing this and submitted right after tnsilver made the same recommendation.) Then, select PURE DIRECT, NOT STREAM DIRECT and it should be as good as it's going to get with this particular receiver. If the problem persists, then I'm thinking rothwellaudio is on the right track in suggesting some really low frequencies that may be causing the issue. However......you also stated that you've been running this setup for a number of years and just recently have been having the problem. This suggests something within the receiver is not well and I know this is not what you want to hear, but it's certainly possible. The only change you made is the new stylus, yet you also tried an older one that exhibited the same symptoms so that leads me to suspect something in the receiver is amiss unless you made other changes that you have not yet mentioned? Might you have changed the location of the turntable in a way that results in less isolation?
Isn't this fun??? I'm about ready to retire the Rotel for my phono listening and get an all-analog preamp that I'll then feed to either the Rotel power amp or a new, perhaps tube power amp. Black Ice Audio is making some really nice stuff and it's way affordable compared to a lot of the other brands. But that's getting ahead of ourselves and you have things to try first. Let us know if you find anything more in your tests.