Whenever we have problems like this, we always start from a clean slate. 1) Have IT remove you from BES. 2) Wipe the handheld. 3) Probably not needed, but pull the batt for ~ 30 seconds & reinsert. 4) Have IT add you back to BES. 5) Reactivate, making sure not to mess with it during the activation.
Using Desktop Manager should not cause any problems. We have users who use it and users who don't, both with no issues. Sounds like something got screwed up during activation...