Also make sure that CGWatcher and cgminer are not inside any of the following folders, because it can cause permission issues when CGWatcher is trying to write to the temporary config file it uses:
C:\Program Files
C:\Program Files (x86)
C:\ProgramData
C:\Windows
C:\Users\
But CGWatcher doesn't do anything pool-specific. I've used coinotron as recently as a week ago while using CGWatcher. If the stats on coinotron didn't show a hashrate, I'd guess it was a coinotron issue. CGWatcher reports the hashrate that cgminer tells it. If cgminer is reporting a hashrate and accepted shares, then it's probably an issue with the pool's frontend. Also, as you may already know, pools generally update reported hashrates at intervals like 5 minutes, 10 minutes, etc.