Both Z3TA+ and Rapture Pro are doing the same thing.
 
Both registry files state 96Khz.
Open either of them as a stand-alone, choose any program and all the notes plays at a pitch that's sound too high.
If any arp/delays are used then they are too fast, as though the bpm is set at 200+.
 
The sample rate on the Roland Quad-Capture has not changed, it's still stating it as being 96Khz
 
To solve this....
The only single thing I do is choose 96Khz from the Sample Rate menu.
I don't exit/shut the synth down.
Everything is now as it should be.
Notes are now at the correct pitch and any arps/delays etc are all at the correct speed.
 
If I close/exit Z3TA+ (or RapPro) and check the registry, they still both state 96KHz.
 
Re-open them and I have to go through the whole process again.
Grrrr.

This may be worth a shot: Open the Microhost standalone, and press Shift+F4 (function key).  If the driver mode is unsupported, you should get an error message (... reset to 44.1K). If not, it may force 96K to stick on the next instantiation.

One thing you could try is running ASIO4ALL for Z3TA+/Rapture's microhost. I've seen some odd behavior with Roland drivers, so ASIO4ALL would get around that and still utilize your Quad-Capture. 

ASIO4ALL works.
Must be a Roland driver issue.