Sorry to read that PRicho has the problem dramatically appearing some more - that is the way it has happened at the school here, quite randomly and across new and old laptops willy-nillly. The fix that a visiting technician came up with pending a proper solution was to use another mapped drive since the problem seemed to be to do with the My Documents folder - however, I think someone wrote earlier that this fix had not worked for them - it has mostly worked for us here with about 3 laptops plus, though I have got the problem recurring even then with one user apparently, not sure yet of what is happening in that single case.
In case I am doing something wrong, I shall mention here how I understand the offline thing should be done - the settings in the group policy are set to allow offline files and syncing when logging on/off, after these settings are applied, I then find that I need to log in the laptop/user a few times and also to log in offline and clich the synchronize option on the right click menu of My Documents, before the settings will properly start working, then after a few logons and logoffs, eventually the files get put across and are available offline. Not sure why in this process at one stage the folders become available offline but not the files, and then after another one or two logon/logoffs the files are eventually there too.
Within this scenario, something else that causes chaos, is when machines do freeze up offline and users have to use the on/off button to get anywhere, then the syncing online comes up with all the 'do you want to keep local or network copy' dialog, and often when looking at the two copies they appear the same anyway - I assume it is something to do with the timestamps being odd due to the uncomfortable shut downs needed.