I'm thinking the tool you're using can't validate the drive that it itself is stored on. Sort of like if you store the repair tool on Foo: it can't validate Foo:, you need to store it on Foo2: .

Maybe I missed it but have you tried creating a "recovery" boot disk floppy, with just enough gubbins to load the OS and the recovery tool, and run it off the floppy? Just a wild guess there, probably still better to perform the validation in another Miggy.
Damned Amiga hard disk validation errors, 10 years ago I blew up my A1200 that way, which had years of custom configuration work done on it, when some disk operation created a recursive listing, sort of like Stuff:stuff\, Stuff:stuff\stuff, Stuff:stuff\stuff\stuff... etc., it got so deep that when it tried to reboot and validate itself it just guru'd. If I'd only had another Amiga on-hand to validate it with, I probably wouldn't have left the Amiga scene for 10 years! :p
Edit: sorry if this seems obvious why we keep suggesting it, but your signature does list an A1000, A2000, and A1200 - surely one of those can act as a host to perform the validation??