I was struggling with custom-post-type rewrite rules and finally found out that multi-page-toolkit plugin was the one that messed-up rewrite rules by flushing them on INIT! of course i put to rest another mystery - every blog page generated a massive 500+ queries, which doubled loading time.
Proposed solution - assign
allpage_permalinkfunction to another action so that it plays well with other plugins and don't generate unnecessary queries.