OK I did some investigating on the issue with iomanX.irx. I can safely say that
it is do to some changes that herben submitted back in February. I recompiled the module using the older source for iomanX.c file dated October 11, 2004. That binary matched the IomanX module we are currently using so there you have it. Maybe it could be possible to fix the partition display mess on the LaunchELF end but I'm not sure. At least we know where the culprit is.
Location of the file in the sdk is for those who are interested:
Now if only we could understand the ps2dev9 issues as well. :(