It might be useful to know which keys were changed.

scook
It might be useful to know which keys were changed.

I just did a system restore from an acronis image and repeated the process to narrow down the culprit. It was a single directory location that had not migrated.
 
HKEY_LOCAL_MACHINE\SOFTWARE\Cakewalk Music Software.  The registry entry is ContentDir. 
 
Note that this will also change the directory to which Sonar installers write application content (not you Scook and Sander- pretty sure you both already know that).
 
Also ensure that the contents of that directory is copied from the old drive to the new location.

Thanks.

I think it may have been the external disk! I was just about to update to say that my problem mysteriously disappeared but upon reading about the external disk I figure that must've been it! I've since installed it inside the laptop so it won't be an issue anymore.

Cool! Happy campers all round. The key in the post above fixed the issue on 2 laptops for me so I am pretty glad you started the thread. It was one of those annoying things that wasn't quite annoying enough to motivate exploration without help and encouragement:)
 
Thanks for the input Scook.