OK, I read up about the Host Protected Area
and I guess that explains why my first 100 GB hard disk appeared to be only 98.5 GB. HPA isn't a Dell-specific thing, it's actually part of the ATA standard, since ATA-4. Dell has either stopped using HPA or only uses it sometimes, because the Inspiron 6400 I just bought didn't have one. MD3 was installed in an extended partition that was perfectly visible in the Windows disk manager.
I would upload the MD3 image, but as jim6172 points out that would be illegal, and also it is huge. Anyway, as I said before I don't really see the point of MD3, it's just a waste of hard disk space.
jim6172, I think you could reclaim the lost space from the HPA using TAFT
. Otherwise a disk wipe with the appropriate tool (e.g. DFT for Hitachi drives) might do the trick?