Hi Florian,
Is there some timeout or maintenance script running only all five minutes that could cause this?
Sounds like a caching related problem. See http://www.mediawiki.org/wiki/Manual:Cache for further information.
You might also have a look at http://www.mediawiki.org/wiki/Manual:Job_queue and http://www.mediawiki.org/wiki/Manual:$wgJobRunRate which regard to periodically run job in MediaWiki.
hth Frank