> and also having to re-enter my registration key after x amount of time had passed
> I have to re-enter it every time I start the MakeCD. What am I doing wrong?
AFAIK MakeCD makes use of the fib_DiskKey field of the FileInfoBlock and encodes it into the registration. Usually this key contains the block number of the fileheader block of a file (OFS/FFS). This means, whenever you do a Reorg or copy the file around, this info will change and you will be prompted for the reg info again. Also, some other file systems or emulation (what WinUAE does with this field I don't know) might have problems returning stable info in that field.