There isn't much we can do to help in this case. As you say XMetaL is working fine until the SDL bridge is installed. None of these messages are coming from XMetaL.
A little googling turns up a few pages discussing problems with machine.config and the reliance of completely unrelated software on .NET 2.0, with the resolution being to reinstall .NET 2.0. Here's an example:
http://social.answers.microsoft.com/Forums/en-US/xprepair/thread/52e9dd11-78c6-4b07-809e-11f7b6cf81eeMy google search was simply for this: "c:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\CONFIG"
Perhaps best to try that as a first step, then follow up with SDL to see if they can help you troubleshoot the errors if they persist.