If this is clean WB install there should not be ANY issues, with exception of all this random issues

. If this is clean install SS should be fine.
IMO this is some sort of HDD issues (BTW. I never had maxtransfer issues

).
Can you write EXACTLY what is in you A1200? HDD size is it CF memory? FastATA etc. Size of first partition?
Are your floppy discs super old/new?