Here is another big issue I stumbled over in another forum which could explain my still ongoing bouncing issues with Studio One 3.3.1.

The issue:
Automation timing depends on the buffer size you use for exporting your mix.
This means your automation timing differs every time in relation to your buffer size. In other words your mix can sound very(!) different every time you use another buffer size for your export.
This should not be the case, as the computer has plenty of time (regardless of the buffer size) for an offline(!) bounce.
The worse thing is that I can't get the automation "on time" no matter what buffer size I use for. The automation is either too early or too late but never on time. Tested from 2048 samples down to 32 samples. The most accurate seems to be 64 samples in my case.

This is on Mac OS X 10.11.6 (El Capitan) with Studio one 3.3.1 (newest version) and different audio interfaces (so it's not a hardware / driver related issue). This seems to happen on Windows based systems as well.

This does not happen with with Ableton Live on the same system with the same settings. The automation is pretty much down to the point, no matter what buffer size I use for exporting in these programs (I know this wasn't always the case in earlier versions but today it is).

In the following screenshots you see a snare sample with a Mixverb inserted. There is a bypass automation at the end of the first 16th note. So the reverb tail should be end exactly on the end of the 16th note.
Watch what happens when exporting with different buffer sizes (see track name for buffer size).
The automation is completely unreliable. I am not talking about a few ticks or samples here. There is a shift up to 64th note (at 120 BPM) when exporting with 2048 samples: