Hi talktwomey,
You might be better severed opening a support case for this issue. Most likely this will require a full set of web agent logs, web agent trace logs, web server logs and event logs to find the root cause of this issue.
The information provided so far is not really enough to even point you in a direction.
I have seen this type of thing in a couple of cases:
1) when IIS had been "Hardened" With tools such as URLScan and removing of the host header information.
2) from the ISAPI filter being installed twice.
3) When the application pool is in 64 bit mode but a 32-bit web agent is trying to be used.
In order to look into this further we would need all of the following either here on in a support case:
1) Web agent version and bit level?
2) Web Server OS type version and bit level?
3) What user is being used for the App pool?
4) What Bit level is the App pool?
5) Web agent logs
6) Web agent trace logs
7) An HTTP header trace, preferably using Fiddler2
Once some more details are provided we might be able to point you to the root cause of this problem and help you solve it.
Hope this helps
Gene