Ok, this is easy too. Just follow the following steps.
Open the command prompt window, run IISAPP to get a list of the current instances of W3WP.exe.
Note the PID of the instance that corresponds to your web application.
Now return to VS, select Debug -> Attach to process and attach to the W3wp.exe instance with an ID equivalent to the PID you got in step 2 -> click Attach.
Now you can trace through the code and find the error causes easily.
But the question still remains, why sometimes are they more than one w3wp.exe instance? This is because the SharePoint Administration Site Collection and the SSP Administration site always have their own Application pools for error isolation purposes.