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IIS 6 with about 25 sites, one of which is .net framework 2.0 with a .net framework 4.0 app below it running mvc 3 in its own app pool. It runs fine for some time, then we see event 1062 and the .net 4 app won't respond until the app pool is recycled. Every time I've seen 1062 in the past the app won't event come up once - what could be causing this?

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It's a race condition. The first one to run wins. You'll need to break the 4.0 app into its own app pool. Here's a writeup on this that I wrote a few years ago, but is still applicable today (for IIS6):

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