What client (broweser) do you experience this in?

can you test other versions and/or other browsers?

I've noticed this before, especially in Firefox with multiple other tabs open. It's caused by a slow javascript engine, usually a result of the browser not having enough resources or too many items open at once. Esp FF is vulnerable because it uses a monolithic threading system, so it's processing all your tabs one after the other each second, resulting in periods where JS has not yet evaluated on your new page. There's not really anything Mantis can do about it, but I have noticed it happens much less often in Firefox 3, which has a lot of performance enhancements.

We use IE7 on XP SP2. (Tested with Firefox on XP too).
This occures since v1.1.1, in our previously productive version v1.0.0rc2 this wasn't visible.
It seems, that somesthing in the filter-showing-process has changed, because it doesn't matter if you have left Mantis with filter collapsed or expanded, Mantis will start with open filters first and apply your settings later.

Maybe it would be better to start always with collapsed filters and open/expand it only for those who need it. That would prevent the "flickering".

Hint: The same IE7 on the same XP and PC doesn't show this behaviour in this official mantis-bugtracker! Could it be, that this version has already some SVN-Changes running?

Hmm, as far as I know, this tracker is a stock version of 1.1.1, or else the version tag at the bottom would report something like 1.1.x-SVN. Perhaps it has something to do with browser caching, eg, is it caching the javascript from mantisbt.org, but not the javascript from your local server? Needing to fetch the javascript everytime could easily be the cause.

Since I personally only use Apache, perhaps IIS is sending some headers or something that prevent your browser from caching certain objects that it should be, or something or the sort?

I don't exclude a caching-problem on our IIS. But on the side "IIS", we have changed nothing.

We have upgraded PHP from 4.x to 5.2.5 and Mantis from 1.0.0rc2 to 1.1.1
Are there any known settings in PHP and Javascript that I could check?

This should be resolved by issue 0009025 when I get the OK to commit it. It will of course only be fixed in 1.2.x though, as it's a feature, not a bug fix.

See issue 0009025.