Running Exchange 2003 and SharePoint Services on the same machine can be a challenge, as is well documented:
I recently tried to accomplish this, but without much success.
First some background. I was trying to run Exchange 2003 Standard Edition with OWA/OMA and EAS and SharePoint Services 2.0 on the same server, which was also a Domain Controller. Actually, it was the only server in the network.
Things started out great, I installed Exchange and performed the steps outlines in KB817379 (http://support.microsoft.com/kb/817379/), which I had to do to get OMA and EAS to work since I did not have a Front-End Exchange server. After testing all the Exchange services I proceeded with installing SharePoint Services. It installed without incident, but then the trouble started. OWA was not working, the same for OMA and EAS. WSS, however, was working. I started troubleshooting and soon found the article I linked to at the beginning of this post. Following the steps in it I was able to get OWA working, but not OMA and EAS. Every time I tried to sync a phone or access OMA I got an error in the event log that said HTTP 400 Bad request. Bad request means a malformed request was sent to the server.
Literally, for days, I search the net and finally had to put in a call to Microsoft PSS. The technician and I spent even more days looking at logfiles and traces of communication between server and clients. We were stomped. I was seriously beginning to contemplate reinstalling the server from scratch. But then we found something.
If you read article KB817379, in step 21 you see the value of the new VDir registry key you will create. Not that the article explicitly states that it should be /exchange-oma, with a forward slash. When we looked at the trace logs from Exchange we found this:
As you can see we had double forward slashes. This was the cause of the Bad Request message. An HTTP GET requestcontaining two slahes is obviously malformed. When I removed the slash from the VDir value in the registry and restarted IIS all services worked.
When this problem was resovled I installed the ActiveSync Mobile Administrator. That was also pretty hard to get working together with WSS, but I succeded.