Dear Kwillis,
The problem is that it happens only on some computers and for very few customers, thus it is very difficult to trace the problem.
I would like to know the following from you:
1) Does the problem occur with quotas administrator account. If you are not sure, please enable them and try for some time.
2) If you enable quotas for user and restart the PC, does the <enable quotas> checkbox is still checked?
3) Did you enable quotas while logged as Administrator or as user.
After I have your answers, we might be able to improve this.
As for now the alternative would be to engage the Schedule feature as well to at least set some bounds.