Hmm.. I have one 40G hd as one big partition with SFS and it works fine. Although I had to disable the automount from it and mount the partition in setpatch with latemount in devs:nsdpatch.cfg. Otherwise there comes problems in cold boot, because setpatch (or blizkick) hasn't updated the scsi.device yet. I don't know if you've tried that too or could it help...
I never have had problems copying lots of stuff with sfs... if there isn't bugs in newer SFS's. I've been using 1.84.
PFS3 is another option. If you use DirectSCSI version of it, then there shouldn't be any problems with anything else. Doen't matter which scsi.device you have etc.
And you have probably double checked the scsi.device too
That it's updated for sure.. ie not disabled with some setpatch option or missing amigaos rom update file in devs or similar
