Soulburned
I work with Ableton Live 9 (9.5 now), as well as Pro Tools and I've run into the occasional "drop out of sync" in both when loading a plugin during playback or enabling/disabling a plugin etc.

That is surprising. Well, if this was not possible, I am sure some operations could be changed to avoid breaking the sync...
 
Tonight, I was trying different loops on a project and every time Sonar started the preview, all my kicks went of sync. So even if gapless audio was not possible, it feels like way too many operations are affecting the audio engine today, which should not.