Hello,
I know the problem. I had the same with the zimreader.
If you use relative URLs you have to take care about articles, which
contain '/'. Look at e.g.
http://de.wikipedia.org/wiki/BMW_501/502. In a
zim file this will be /A/BMW_501/502. Relative urls must point to
../something or ../../A/something. If you have a link to e.g. BMW_505 it
points as a relative url to /A/BWM_501/BMW_505.
But yes, relative urls are much better.
Tommi