I had the same problem and I think I resolved it.
Try this fix.. also located here: Exchange ActiveSync & Hotmail - HTC Thunderbolt (Verizon) - Android Forums - HTC Community
Turns out all I had to do was:
1. Delete the account on my Thunderbolt
2. Empty out my Hotmail/Live inbox completely
3. Re-boot phone
4. Setup the account again on my Thunderbolt
5. Send myself a test message, from myself
I think the trick was emptying out the inbox, but I just wanted to be sure.
Try this fix.. also located here: Exchange ActiveSync & Hotmail - HTC Thunderbolt (Verizon) - Android Forums - HTC Community
Turns out all I had to do was:
1. Delete the account on my Thunderbolt
2. Empty out my Hotmail/Live inbox completely
3. Re-boot phone
4. Setup the account again on my Thunderbolt
5. Send myself a test message, from myself
I think the trick was emptying out the inbox, but I just wanted to be sure.