I finally got a look at your logs and what's happening is the MS application compatibility usage is interfering with the module reporting process within the jpe dll. That's because app compatibility uses a set of dlls which use Detours, MS's own api-hooking library. If you look at your logs you'll see that every single api call that jpe is reporting on indicates that it's coming from "aclayers.dll", which is the main api-hooking dll for the app compatibility layer. So, that's the problem.
For now, what you could do is add "2=aclayers.dll" to your [ModuleInclude] list and that should get your current jpe runtime ini working, albeit slower than it could be.
There's 2 things I'm going to do. First, I'll always force any api call made from aclayers.dll to never be excluded. That should prevent any problems in the future. Second, I'm going to make up a .zip for you to download that will have a new "Foxit Reader_portable.exe" in it that will run without the need for the app compatibility set to XP. So you should be able to run it as normal and then see through the logging output whether or not the calling module is reported correctly. If so then you should be running on Vista just as if you were on XP.
EDIT:
Here's a link to a "new" JPE-created portable app launcher that should allow you to run Foxit on Vista via JPE without having to set any app compatibility settings. The launcher expects the jpe & mch dlls to be in the app directory and was created with in-memory registry redirection and no file system redirection as its defaults.
It would be nice if you could run it with the jpe log dll to verify that the module names now show up as something different than aclayers.dll. I've also included the jpe runtime ini that I use with Foxit that includes a few more registry inclusions than yours had.
BTW, you can use this portable app launcher with any other Vista apps as well. Just make a copy of it and rename the copy to %appname%_portable.exe. You'll obviously need a different jpe runtime ini, especially if you want file system redirection turned on. The launcher will also launch apps that are named %appname%.jpe, if you want to prevent the non-portable app from being accidentally executed. If you do that, you can also rename the launcher to just %appname%.exe. But make sure you always have %appname%.jpe in your module inclusion list if you rename things as above and you also use "exclude all modules". The included jpe runtime ini has this already set up for you if the above is confusing. Just take a look at it to see what I mean. You'll need to edit it anyway, if you want to use it, since it's storing the .reg in the app directory and IIRC you had yours stored elsewhere.