Radek,
Instead of setting the security level of the VIs themselves, set the security level of the folder where the VIs are saved. I've seen this unusual behavior before when Win2000 would assign the saved VIs the same permission as the temp folder, not the folder the VIs are saved in.
To get around this, you should assign your desired security on the folder that contains VIs instead of the VIs themselves. Set the security of the LabVIEW temp directory to be the least amount of security that is acceptable (this must be less than or equal to that set on the VI directories). By doing this, the VIs that are saved will have their permissions set to that of the temp directory, but security on the directory containing the VIs will filter unauthorized users from acce
ssing the files.
The only reason I could think of why you have different behavior on the two drives, is because of the different permissions of the temp folder on those two drives.
Zvezdana S.