have a samsung 20gb h/d in it
...
all worked in 3.1
I strongly doubt that. You cannot use a HDD bigger than 4GB with 3.1 only. You need 3.5 or 3.9 for that and you have to partition the drive from a running 3.5 or 3.9 system. That's what the emergency floppy disk is for.
Please run
Check4GB and post its output here.
The least you have to do to resolve the situation is to run HDToolbox, go to Partition Drive, then to Add/Update and update FastFileSystem to the version coming with OS3.9.
After that, either the hidden partitions appear again or you have to reformat them. Run Sys:System/Format and choose the partition to format from the list.
And you should install at least Boingbag 1 for OS3.9.
Bye,
Thomas