All versions of genuine Ghost (i.e., not the current consumer "Norton Ghost" which is now a different product using our brand) we've released are backwards compatible; new versions generally contain extensions to the .GHO file format (so old versions of Ghost may not necessarily read newer .GHO files), but the base .GHO file format used currently dates from Ghost 3.0 - ensuring that old images can be restored is a part of our standard internal build testing.
As I said it's not particularly a "problem" at all; all Windows versions since 2000 can report this when the disc signature is zeroed and it has no deleterious effect other than the notification, which is harmless in itself. You are just seeing the effect of faster hardware overcoming the large delays in Server edition startup compared to desktop editions, which will be what masked the notification from being generated in your case.
The only actual, as opposed to cosmetic, effect of this zeroing is that drive letter assignments are regenerated (as custom drive letter assignments use the Disk ID to identify the source partition) back to the Windows installation defaults. This is a non-issue for manufacturing and almost all backup scenarios, but the disk signature preserve switch is there for the rare backup scenarios where customers have used non-factory custom drive letters and want them perfectly preserved on restore.
To answer your second question, it is indeed the restore process triggering the notification; as explained, restoring by default zeroes a fingerprint in the MBR that Windows uses to identify disks. Altering the disk signature is a useful thing to do (especially in manufacturing) as there are very negative results that can occur from two disks with identical MBR signatures being present in an enclosure at once, which is why generating a new disk signature is important during manufacturing scenarios and thus why this was the default action on disk restore.
If you are using Ghost in a manufacturing scenario then you be using the one-time VAR license model rather than the per-seat model which is sold through the online store. You should contact Symantec's sales staff for that as VAR license contracts offer a range of different approaches supporting different manufacturing volumes (and since manufacturing volumes are more volatile than seated licenses, there are license models which have more purchase flexibility).