I have spent a little time looking into this problem, and here's what I found:
1. The 8.2.1 format disk is approximately 96% full, whereas the safemode disk is approximately 75% full. Not sure if that makes any difference, but it might with the next bits of information.
2. If I copy the safemode.exe from the format disk to the safemode disk, the safemode disk still works just fine (and, to be honest with you, they're the same file).
3. I formatted a PC desktop with the format disk, which copies safemode.exe to the hard disk. I then booted the system with a safemode disk, and FTP'd the safemode.exe on the target over to my host computer. When I perform a diff of the safemode.exe that is copied to the target and the safemode.exe on the format floppy disk, the last several kilobytes of the file from the target is absolute junk.
Inside of safemode.exe is a compressed file system containing all of the RT Ethernet drivers (along with other files and settings necessary to boot a target, basically everything within ni-rt/system/... on an installed target) and if that compressed file system image gets corrupted then the system cannot mount the compressed file system. In cases like this, it's like deleting the ethernet drivers from a running system - when you reboot you immediately get the, "Unable to find primary ethernet device" message because it cannot load any of the ethernet drivers to actually determine if there are any ethernet cards in the system.
While playing around, I found that I have around a 50% likelihood of running into this if I load the disk to 90% plus capacity - the problem occurs in different files (judging from the diffs of the written files) depending on how they're written to disk, which might point out a problem with caching in the floppy disk filesystem manager. I say only the floppy disk because I have yet to reproduce this with 16 and 32 bit FAT systems, but the problem is very reproducible with the 12 bit floppy filesystems.
We will investigate this issue further, thanks so much for bringing this to our attention!
-Danny