Heya pkward88,
definitely doesn't happen that way here with Pianoteq (in other DAWs - I don't recently use Logic) unless there's a mismatch in settings (host project, interface, Pianoteq, any other loaded system audio getting in the way). I suspect you'll find the odd thing out in short thrift, or just overlooked a check-box in Logic somewhere?
Forgive if the options are not relevant to your situation (or you're aware of them and tried them already.)
Some more info would really be needed to trouble-shoot but sounds like maybe you're correctly set at 48kHz "sample rate" - but are you working at 32 bit inside Logic? (I like to work with 32 bit float, 24 if complexity pushes the system too far, then when bouncing/exporting etc.. I might go to 24 - then I can still re-work something if needed without damaging or creating artifacts in the down sized audio). Output to whatever final rate you want - but it should still sound quite close to the original even at 16bit CD rates. But with extreme downsizing, dithering might become more important to test and A/B.
Then when exporting (down) to 24 bit rate and 48kHz sample rate which would likely invoke some choice about dithering, no dithering and/or normalization which might need a few changes for best results. I believe Logic's export window should allow you to choose the type of dither and if you want normalized output in real time? Trial and error and your eventual taste will decide - and some others who use Logic a lot might have their own wealth of experience with its settings.
Other ideas - if you've done lots of editing of an Pianoteq (or any other audio) track, and in that process, you have changed down the rates, some plugin or the DAW might have auto-applied some dithering (check DAW settings for things like "automatically dither on mixdown" or similar). If every time you bounce a new version of a track (say with newly added reverb) it may still sound fine in Logic.. but when you go to bounce/export a final mixdown, it might be adding dithering yet again to that already dithered audio for the maybe 3rd time? You will maybe hear flatter response, maybe some noise like old analog gear or bad leads, glitchy or gritty, less headroom perhaps, some collapsing of frequencies into each other, rather than the nice clean bands you heard while in the DAW. A lot can go wrong. Even if no dither is applied, what should be a nice clean digital sounds, can sound like crushing glass in the background of a downsized file.
Maybe you're listening back to the aif on a different app with its own driver/mixer volume or some other thing lacking compared to Logic?
Or, you use an audio interface with a nice tool to boost/attenuate headroom (RME?) with Logic and Pianoteq but when you're playing back regular audio, it's not in the chain somehow? A button in Logic to monitor, rather than playback, if you have some unique routing.
Related to above, does your audio interface run through some hardware like a nice valve EQ? but that's cut out of the loop when playing back the aif on a system media player?
Or, you put the aif on a thumbdrive and plug it into a home theatre? and sounds un-mixed, or not properly 'mastered' (look to dithering and normalizing etc.. or maybe some mastering tools might be what you actually need - it's a nice learning curve but worth it for outputting better files.)
Is it possible to bounce/export from Logic and be bypassing effects? (In some hosts, there's stuff like "bypass effects when updating mastering file").. or in some instances, an bounce/export/mixdown etc.. can be with or without FX? (if you are running Pianoteq through an FX send/return for reverb or some other important aspect of the production).
Without more details, I'm more or less out of obvious ideas right now but sincerely hope something here and the above post helps you get to the issue.
Pianoteq Studio Bundle (Pro plus all instruments) - Kawai MP11 digital piano - Yamaha HS8 monitors