That shows that IDEFix is working. Because the standard 3.1 ROMS has no ability to detect HDD over 4GB it will only detect the first 4gb of your HDD. If your first partition is 2GB and the second is > than 2GB it will not detect your second partition and all subsequent partitions. However when you do a soft reboot IDEFix has already patched your system to accept >4GB HDD which is why it is recognising the other partitions. Try getting ffstd64.lha Even though you don't use FFS it might help but i doubt it. 3.1 just wasn't built for large HDD's.
I would now like to hand you over to our friend Bloodwych in a thread on EAB. Here.