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Have you made sure that both CRM and WSS use a different App Pool? They should be in different app pools by default, but wouldnt hurt to check.
What about the Service Name used to run each App Pool? I have had issues (random ones) if I use the Network Services account for all of my App Pools. I've recently gotten into the habit of defining new Services (like CRMService or SharepointService) and using the those new service names.
This does add one additional burden of making sure that each new service account that you create has the proper security credentials.
For troubleshooting purposes, you could use an "Administrator" type account on one App Pool, and then use a different "Administrator" type account for the other App Pool. Restart IIS and all services and see if that helps identify the issue.
Hope some of that helps spark a solution.
thank you for your reply. I think I got this working now. I cannot tell exactly what the problem was, but It seemed like the sharepointsite had multiple IPs assigned (its a separate dialog in IIS6 config). I came into this by accident only.
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