Sometime, I need to debug into web service from my portal. It is easy to get an error dialog telling something like "cannot automatically debug into server" when you step in the web method. After I make 100% sure that the pdbs are absolutely in sync with the dlls, I did two things to make it work:
(1) enable debug in all web.config files.
(2) specifiy the symbols path in the project options.
Another time, when I debug from my portal to web service A and to web service B, service B prompt the same error dialog. I thought it is unsync PDB problem again. But after checking the event log, I found the cert expired for service B. After renewing the cert, I can debug into B.