Do you mean you get an actual time-out error message (e.g. about the connection to the database) or does it just halt somehow when you leave the program open all night?
When you look under Tree | Watch Folders, do you see any "Currently watched folders" - and, if so, is there any activity in any of those folders during the night (or in the current folder, for that matter)?
You could try turning off any folder watching, and for the current folder, turn this off: "Options | Preferences | Thumbnail View | File Options:Watch changes in folder". With that done, I can't think of any other ongoing background activities that could somehow cause TP to crash. Is the Task List empty when you leave the PC overnight?
Maybe it's caused by some Windows activity reflected in the tree panel.. for instance, if you don't need to see any network stuff there, you could go to Options | Preferences | Disks & Folders and mark "Do not show the network branch" and in the bottom section you could turn off display of 'public locations'. I'll let you know if anything else comes to mind.