You are having the SAME problem I am. I have disabled Sense UI and restarted the phone, as it wouldn't close until I did. I was then using just the basic Android Home and it showed about 125 free mb. BUT Linux is telling me I only have access to 186 MB of ram total. It's like the system can't access the rest of the ram. Sort of like the issue with the N1. I've posted a topic at howard forums. Lets see if we can get this resolved between the two websites.
HowardForums: Your Mobile Phone Community & Resource - missing ram?