Andrew, exactly what method are you using to create the portable launcher? If you're using the command line, as Chris did, the path to the app's executable needs to be in double quotes, as "Foxit Reader.exe" has a space in it. This is kind of command line usage 101 and is not specific to JPE so I forgot to mention that in the readme.
OK, after nearly tearing my hair out, I finally figured out what was causing the problem, and how to workaround it.
I have two drive letters, C: and V:. V: is actually a subst of C:\personal.
Now, JPE is located in V:\apps\jauntepe\jauntepe.exe.
Foxit Reader is located in C:\test\foxit\Foxit Reader.exe.
If I launch JPE using PStart (path is ..\jauntepe\jauntepe.exe), then I drag-and-drop Foxit Reader.exe to JPE, then I right-click to build portable EXE, the first path I see is:
?:\test\foxit\Foxit Reader.exe
and I get the "Invalid EXE" message.
It makes no difference if I set the "Home directory" field for JPE under PStart.
However, if I launch JPE directly via Windows Explorer or equivalent, I don't get this error anymore.
If I drag any EXE from V: to JPE launched via PStart, everything is OK too. I get the correct drive letter instead of the '?' character in front.
Crazy huh?