So I'm new to PRSs, but certainly not to guitar and maintenance. "back in the day" I even worked as a luthier and repair man - so I've done my fair share of setups on strats, gibby's, floyd-type guitars, etc... But never on a PRS. Fast forward to now and I've been enjoying my own very first CU24 for about 2 months and decided to do a bit of setup. Well the high e string seemed a tad high and the was as far down as the height screws allowed (saddle resting on the bridge plate). So I did the logical thing and lowered the bridge via the 6 screws. I "only" went 1/2 turn (on all six) and then backed up about 1/4 turn. Now of course I never rtfm'd - where it clearly states that one should never adjust those screws while there's tension on the bridge lest you dull the knife edge. Now it seems I've got a slight bit of tuning problems and cant really tell if it's because my bonehead move or a result of one ore more of the following....

1) tuning to Eb
2) switching to 9 gauge strings
3) using a different brand strings (D'Adarrio - used for 25 years)
4) generally wonkiness with floating trems

I've dealt with bridge related "edge" tuning problems. These can usually be identified by tuning to pitch and then gently depressing the bar / check pitch and then gently pulling up on the bar / check pitch = if there's no fluctuation then it's usually not bridge related. My problem seems to be that I play for a few moments and then check tuning and one or more strings is out. Also, it doesn't seem consistent as to any particular string...

Any suggestions?