According to the developer of Resource Hacker, this product is discontinued (and hasn't been updated since Sep 2011):
I have been overwhelmed by the interest in Resource HackerTM, the emails of thanks, encouragement and suggestions. It's been downloaded many millions of times. However, I've moved on to other things and have no plans to continue its development. Please don't ask for the source code, I'm not releasing it, nor is it for sale. Colin Wilson has written an open source Resource Editor which may interest those looking for source code. Otherwise, Anders Melander has also created another excellent Resource Editor which is still being developed.
While this is not a direct answer as to why Resource Hacker can't work with some PE files, you may follow the author's suggestion to try out the open-source XN Resource EditorXN Resource Editor or Anders Melander's free Resource Editor.
If you can reproduce the same issues in Colin Wilson's open-source XN Resource Editor, it may be much easier to inspect (via Delphi's debugger) and find the root cause.