I have had this problem with Heidi on a few machines connected to a few database (all of them on Hostgator which may be the key)
After running a query, I have roughly 3 seconds to view or edit the data I want before the whole thing freezes.
Sometimes it just greys out, other times it totally hangs for a few second.
Each time it says disconnected in the bottom right corner. I have updated to latest version, I have downgraded to a very old version, all do the same thing???