First the obvious – check Tools | Account Settings | and check the delivery location (bottom of e-mal tab) to confirm that it’s set to the Inbox.
Barring that, you will need to explain exactly what steps you performed when you say you rebuilt Exchange and IIS, and what switches you ran for Isinteg on your priv.edb. What happened to your server, and why did you have to rebuild Exchange? Why didn’t you restore from backup? Or did you?