Sounds like some problem with your rewrite rules, yes.

It's somewhat undecided whether we want to support this sort of configuration... some would prefer to more aggressively put parameters after $wgArticlePath/$wgActionPaths-style links.

rowan wrote:

I'm not very familiar with Lighttpd, but if I see it right, you make a mistake in your second rewrite rule. You add the query string (the part after the '?' char) to the title, but this will rewrite to (using your example) /w/index.php?title=Special:Searchsearch=foo&fulltext=Search
Clearly, you want to add an ampersand between $1 and $2, but that would also add an unnecessary ampersand if you have an empty query string. I would simply add an extra rule so that you have one for queries WITH query string and one for queries WITHOUT query string.

With Apache's mod_rewrite, I can simply use the qsappend flag to copy the query string over automatically. Doesn't Lighttpd have something similar? In mod_rewrite, this flag will even figure out if it has to use ? or & before the query string.