No, it is not the blank icons. It is when I change icons in a pack and save the package it can happen that for example .jpg extension files have the security shield applied as an icon or that .xlsx files have the .txt icon applied. All sorts of strange things also happen to other Icons also.
I've had that happen to be when I was building a package. I opened the builder, put a few in, saved it, closed it. When I reopened it and added a few more they got all messed up, like IP forgot which icons went where.
I've since been told that it's best to just put all the icons in all at once, not to close and reopen the builder while putting them in. That works for the most part, but even then, not all of the icons will apply ...or even show up in the preview window. And this 'solution' will not work if you only want to change a few in a pack once you've downloaded it.
Iconpackager is definitely in need of some TLC.