Hey dazric,
To me at first your description seemed typical of a "click" at the beginning of a rendered file, often seen on meters but maybe not heard due to whatever out-of-hearing frequencies. (DAWs have different ways of auto-creating "fade in" to avoid start point bumps/pop/clicks, or manually you can do it) but I haven't had that issue with rendered Pianoteq audio - but since this also happens with MIDI, I fired up Reaper to see what else it might be.
When experimenting with Reaper, when continually looping the same section (solo Pianoteq MIDI), the playback of the track can get out of sync with the FX. (I have had this happen with some DAWs - but it seems like a setting might "afix" playback to FX.. just did not find for certain - and got lost in the Wiki TBH).
Someone else using Reaper a lot, might know this setting?
My test recently with a Cocos "voice" plugin which I was just experimenting with (easier to "hear" than visually read the meter 'bump' on a Klanghelm - I use a different Klanghelm one - they're quite nice BTW). The track (Piantoeq) was playing in a looped section (MIDI, not rendered) and as I altered the settings of the voice plugin hearing the changes, when I raised the DRY level of piano (within the plugin UI) to hear it alongside the FX (which I was auditioning WET), then it was playing a half bar out of synch.
The plugin was half a bar late. Maybe the loop happened 20 times or so before I checked the dry piano signal.
I thought "there's just a delay in processing maybe - the FX plugin naturally is rendering a bar late.." - but.. when I stopped playback, began from zero, it was actually now in synch.
I don't like this in a DAW. But, as above..
There are a lot of choices in preferences in Reaper for handling events (I'm not a constant user of it, so still remain unsure how it "glues" things) - but I'd try experimenting - but keep note of "defaults" if you try changing the Reaper's deep settings.
Maybe that was not your workflow though dazric?
Maybe you were not looping the section or something else - but other than some automation going on (accidentally or other), I hope my experiment might shed light - or interest others to provide more experienced Reaper feedback.
Pianoteq Studio Bundle (Pro plus all instruments) - Kawai MP11 digital piano - Yamaha HS8 monitors