at the moment minibb generates different urls for the same main forums like: ../forum/index.php and ./forum/index.php?
Than ? at the end creates a different url and confuses crawlers. You can see the difference in this forum: your index.php file has a pagerank of 6, and index.php? has a pagerank of 4

I suggest changing index.php line:
if(!isset($GLOBALS['indexphp'])) $indexphp='index.php?'; else $indexphp=$GLOBALS['indexphp'];

Remove the ?
and search and replace all {$indexphp}action to {$indexphp}?action in all files

That change will make the forum more search engine friendly.

just one more modification is necessary: search and replace all {$indexphp}sortBy with {$indexphp}?sortBy

that should be all that's necessary

This "?" is required for those people who wants to include the forums index page from their own page.

ok. another workaround is to link to index.php? from the main page. Thus, you won't have index.php and index.php?, but only index.php? (this will concentrate more PageRank in the post pages)

Hmm, remember that not everyone has exactly index.php... Many users rename this file, if their forums are crossing with another scripts.