I doubt count in had anything to do with it.
Sounds like latency
Can you hear the delay between when you hit a key and when you hear the note?

Does the file have audio and MIDI , and this what is out of sync, or is it MIDI to MIDI that is out?
What tempo and resolution was used when it was 23 clicks (thingabobs) behind?

This will allow us to put it into milliseconds and get an idea what it could be..
May be that adjusting the audio buffers will allow lining up.. or it may need latency adjustment.
I believe the help file explains how to use the latency adjustment file included with the program.. if this is the issue.

Have you tried just using the MME drivers or the ASIO drivers designed for your card?
What soundcard is handling the MIDI?
Does the keyboard have a USB MIDI driver available?

I do not work here, but the benefits are still awesome
Make your sound your own!