popup comments & permalinks

Someone please please help me with this. I know it sounds minor to some but I’d really like to get everything uniform … I’ve asked this before and no one could help so I waited a bit and thought someone might have an idea.

I have enabled popup comments and even been able to utilize a custom stylesheet which increased the speed of the popup window. Popup comment windows work fine on initial posts. However, when clicking on a permalink via the archives or an embedded link in a post of mine or on another blog, the post comes up with the embedded comments rather than the popup comments link. How do I fix this? I would like for the permalinks to pull up just the post without the comments appearing on screen automatically just like on the front page.

Any suggestions?? I’m clueless how to fix this (if it can).