Are you using Windows to copy the Amiga system files onto a FAT-formatted CF card, then transferring the files to the Amiga and hoping they will work? Because that could be your problem. Please try this:
Install LHA in 3.9 in WinUAE if you haven't already.
LhA 2.12 (Run this first) -
http://aminet.net/package/util/arc/lhaLhA 2.15 (Then extract this) -
http://aminet.net/package/util/arc/lha_68kThe best way to transfer your system is to pack the entire lot into a LHA archive, which can easily be swapped around on disks without losing any of its original formatting, then extracted onto a real Amiga.
Either mount the CF in WinUAE or make an extra partition temporarily, it can simply be a Windows directory rather than a hardfile. I don't know what your root partition is called, but let's just say it's DH0: and the new partition is DH1:, this is what you should do to make an uncompressed LHA (which will extract much faster than a compressed one when you transfer it over to the Amiga). Open a Shell and type:
DH0:
Lha -eraxz a DH1:Backup
Then it will create a file called "Backup.lha" on your DH1: partition, or whichever one you choose. Don't make the destination drive the same as the one you're archiving, and make sure you have plenty of RAM assigned if you're going to use the Ram Disk instead of a second partition.
Now when that's finished you can copy the Backup.lha file to your CF card from Windows if you didn't already mount it and create the file on it. Put it in your A3000 however you've been doing it (I assume you have a SCSI CF/SD card reader?) and to extract the file back onto a fresh partition in the A3000, using CF0: in this example for where the file is coming from and DH1 as the partition you're extracting to, type this in a Shell:
DH1:
Lha -xa x CF0:Backup.lha
Then the OS3.9 setup will be copied to your A3000 EXACTLY the way it was in WinUAE, without any FAT/Windows butchering.
