My "punch in" does not use the punch in feature. I just play (space bar) and press "R" when I want to record, the press space bar to end it.
I "think" I'm on to an ASIO driver problem (or a problem with ASIO in Sonar) as I just tried WDM and didn't have the problem. I did a reinstall on the Roland Studio Capture drivers but that didn't help. I created a new aud.ini file but that was with the ASIO drivers and that didn't fix it.
As WDM works, I'm going to give the aud.ini another shot. I'm going to delete it, restart Sonar and use the WDM mode. If that works I'm going to switch to ASIO and see if that fixes it. brundelfly's suggestion of the aud.ini seems to be a key or at least a key in this.