This is more a 'why does this work this way' than a 'how do I make this work' sort of question.
I have a WCF web service I am debugging remotely. It is deployed to a staging server where the VS 2010 remote debugger is installed and running as a Windows service. The permissions are correct, I can attach to processes without any problem. The issue I ran into is I couldn't consistently get the symbols to load.
I have the WCF service deployed to C:\Webs\MyService, with assorted DLLs in C:\Webs\MyService\bin. It is set up as a separate site with its own app pool. What I found is even if I had the necessary .pdb file in the bin folder, Visual Studio wouldn't load any symbols when I attached to the w3wp.exe process from my local machine. What was happening is when IIS started and the worker process was spawned, my service DLL would get copied deep under the temp ASP.NET files directory, into something like C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Temporary ASP.NET Files\root\19f82539\e55fff8f\assembly\dl3\2926a261\f625d158_f62ecd01. I found that if I manually copied the .pdb file to this folder, then symbols would be loaded and I could do the debugging.
I'm wondering why the heck it works that way, and how I can avoid having to manually copy the symbol file to this other directory. What's worse is if I had to make changes and redeploy, the worker process wouldn't recognize them. I had to restart IIS which caused a different temp directory to be created, requiring me to copy the .pdb again.
I have a similar problem, with web applications. Apparently Microsoft are aware of this: http://go4answers.webhost4life.com/Example/remote-debugging-symbols-not-loaded-207525.aspx
Hopefully, they will release a fix soon.
There is also a suggestion by BrianR on a related question, Why are no Symbols loaded when remote debugging?, saying to create a folder with the debug files and on the remote server to point the environment variable _NT_SYMBOL_PATH to it.