I just ran into the same problem. Firefox just showed pentadactyl as "enabled" in the extension list, but it wasn't loading it at all. The build from
https://github.com/ffledgling/dactyl-build/releases worked without a problem though (thanks to its author!).
After diffing both xpi files I found that my locally created "config.json" was broken: there was an extra line with unmatched quotes in there. The source file looked fine though, so the make process must have screwed something up.
Turns out it was a problem with my git configuration, which converted all the text files into DOS line ending format via the config setting "core.autocrlf=true" (and until now, I used the mercurial repository). This command fixed it:
git config --global core.autocrlf input
You probably have to delete your local dactyl copy and clone the repository again.