Seems like i did miss something. The first copylock check writes 0000 to the address in the USP (which is $FE). On Kickstart 1.3 A500 this address is always 0000 on every boot so the check at the start of the last level is not triggered. On Kickstart 2 and above this address does not contain 0000 at boot time and bypassing the copylock caused the address to not be cleared and the last level freezes.
I have uploaded a new version to the zone. Only disk 0 has changed as i simply clear out this address in the bootblock and all is good.