I think you should strip that down to a clear, concise bug report and post it in the IconPackager Support forum (if there is such a thing)
There, the devs are almost sure to see it and maybe it can be looked into. Now that SD is refocused on Desktop apps, maybe IP can get a little love.
I love the software but it does have a few quirks.
I've never tried building a package but I use them all the time, so anything that will help you and others create more Icon Packages has got to be a good thing.
P.S. Good one, Jafo.