So you disabled ALL your plugins, activate ONLY comments quicktags and it worked like a charm?
After successfully getting it to work, you then activated all your plugins, one by one, checked output on your site per individual plugin, and now it doesn't work, right?
If that's the case, I'd imagine there's a conflict somewhere with another plugin. By activating them one by one, you'd have come across the conflicting plugin.
Then its just a matter of which plugin is more important to you.
If by some chance your comments plugin didn't work, while having NO OTHER plugin running, I would go back to the original source and download the file again, making sure there's no whitespace if you copy&pasted a text file then converted it into php and upload again.