I have the same issues with my D2. The Exchange integration is terrible.
I have my phone synced with 2 different exchange accounts. 1 Account uses Touchdown and works flawlessly. The other uses the built in "corporate sync BS" Most messages don't show up unless I manually refresh my inbox.
I never had an issue with this exact same setup on my Droid 1...
Google needs to buy Nitro-Desk (makers of Touchdown) and implement the code into Android.