It works OK for me in Lion with the current version of that epub.qlgenerator installed and BetterZIPQL.qlgenerator 1.2 installed.
What version of OS X are you using and what version of epub.qlgenerator are you using?
It looks like https://github.com/jaketmp/ePub-quicklook/downloads
added a new version for Lion, and maybe it isn't completely compatible with older OS Xes? One change is that Lion introduced a UTI for epubs which that epub.qlgenerator had to then also use - UTIs are how Quicklook decide what generator to use so it is important that these all "match up".
(UTIs are used by lots of other apps too, they're not QuickLook specific.)