These _NTFRS folders are called morphed directories and they indicate an FRS
problem. eg they can be created if there is a collision in FRS when the same
object is created simultaneously in two places.
It will most likely be these folders taking up all the space, this KB will
tell you how to remove them safely. You basically have to find which folder
contains the good copy of your data (the morph folder or the 'real' folder)
and then delete the other one.
http://support.microsoft.com/?id=328492
It may also be required to perform a non-authoritative restore of FRS with
the burflags registry key to reinitialise FRS.
Things to check before you do anything:
Make a one off copy of Sysvol, just copy the folder to another location and
make that your backup.
Do a full System State backup
Check the System log for JOURNAL_WRAP errors. If these are present you need
to D2 the server with the burflags key.
http://support.microsoft.com/?id=292438
Install SP4 on all your DC's. There are a lot of FRS hotfixes and changes in
SP3 and SP4.