I hope those 400K disks are copies and not originals, and you have them backed up someplace. NEVER stick anything in an untested drive you don't expect to get trashed.
There could be any number of problems causing the disk incompatibilities in the 800K drives. Since the 400K disk is only read from one side, head alignment is the most likely culprit. The 800K drive shipped with the yellow plastic insert to prevent head damage during shipment as the heads did not park. Most likely this is why it is not properly reading the 800K disks (as both heads have to align to read alternating information from both sides at once). It could also be the 400K/800K switch not recognizing the 800K disk so it doesn't know to read both sides. Your SE could also be slightly out of alignment for the very same reason, though it works perfectly well internally to disks it formats itself. Also note: if your Mac has been running a while and is hot when you make the disks, the media itself could expand causing a misalignment after it cools. The best time to format a disk is when the machine is cool.