This blank icons bug/issue, despite being a well known problem for MANY YEARS (I'm sure Stardock is very much well aware of it), still hasn't been fixed.
I have no idea why IconPackager uses a IconHandler sub-key for exe files, since it doesn't even change the icons for those, but the fact that it does and that it doesn't remove it on uninstall has caused countless grief for many (me included).
Me included not because I use IconPackager but because, as the developer of the Winstep Nexus dock, users blame Nexus for this issue more often than not: 'Oh Nexus is showing blank icons? What a buggy application! Uninstall!'. I even have an entry on the Nexus FAQ for this issue (but who bothers reading FAQs?)
I'm seriously thinking of taking the matter into my own hands, automatically detecting the problem when Nexus runs for the first time and offering the user a fix (clearly pointing the finger at the REAL culprit). Come on, guys!
Stardock knows I usually don't meddle in this kind of stuff, but this has been a real annoyance to me because of users thinking the blank icons problem is a bug in the Winstep applications themselves.