I’m using Cubase 12.0.70 (will upgrade to 13 in April). I have an issue occurring often enough to be a nuisance but not quite often enough to make Cubase unusable. VST instruments, my most frequently used is Omnisphere, are suddenly detuning quite drastically. Omnisphere is well behaved and I can restore proper tuning by deselecting and reselecting the patch. Halion Sonic is less obliging and I can only restore a useful tuning by deleting the instrument and loading a new instance, which means I have virtually stopped using it. Eventually I noticed that it was always the instrument currently selected in the arranger page that was prone to ‘pop’.
I once had something similar. I worried about clocking issues but then realized a synth had a broken pitchbend and was sending out random messages.
Have you eliminated this kind of thing?