I have seen the installers for codec packs ask if I want to remove what they think are invalid registry entries. Luckily, I read the info before clicking delete and noticed they were referencing the cakewalk dll's for the pro-channel modules and chose to leave them alone. 
 
Be advised! Glad you found a solution.

I use ccleaners reg cleaner only if I have installed/uninstalled many programs.
I always back it up as well.
but I reinstall wondows every 2 months to keep a clean fresh system.
I have a back up made of windows installed with all updates and sonar installed with plug ins.
this was done error free.
 
now I just reinstall this once every 2 months.
its also good for clutter control of useless docs saved over the past months.
my daw is also a split surfer, documents maker/exc.
 
all this talk of my daw doesn't go on the net, my daw is for music only is great but
in my experience in the last 5 years alone.
I have both, a daw machine, and a daw that's also used as a surfer(not notty videos either)
just surfing, email, cakewalk forums, no games though.
 
ive seen little difference enough to make me use my own dedicated pc for daw only.
well you could catch a virus, 5 years now. malware yes, adware yes, the FBI virus, no.
I back up.

Any legit site has the potential to have a virus. These forums (running third party code) could suffer from a SQL injection attack for instance (therefore applications security updates are common). Any web page could also link to something dodgy, any page. The fact is right now you probably have absolutely no idea if you have a virus or not.
 
You can install a virus scanner with little impact nowadays and you can exclude folders MS recommends plus get your DAW from any real time scanner.
 
>  the FBI virus, no
 
Not yet, also you may (or may not)  be aware that this thing can travel over network shares and USB cables where your backups are. As there are millions of viruses out there the chances of getting that over the others may be quite slim.
 
The choice is yours of course but I definitely wouldn't do it, in my view virus scanners should be made compulsory by law, I get enough zombies as it is sending me junk mail (mainly from Florida it seems where the old folk don't bother updating and are continuously browsing porn ).

Hm I wonder if the registry cleaner "cleaned" more than just the registry.
Modules failing to load would more likely  be caused by something removing prochannel modules than changes to the registry.
For prochannel modules the only thing in the registry I know of is the default GUID's that define which ones are loaded on a bus or track.
You could probably restore the registry state by forcing SONAR to re-personalize - I think launching the app while holding down CTRL does that.