I don't see this.
- Extension manager correctly touching conf/local.php on both enabling & disabling plugins (blame shows since 2013-08-02, https://github.com/splitbrain/dokuwiki/commit/02779b18797b2ee1304613de684d54988815dacb#diff-441b0afb846829ac54893372ccbaa72cR503
- tpl_metaheaders() correctly adding a tseed value based on filemtimes of config files (blame shows since 2013-07-31, https://github.com/splitbrain/dokuwiki/commit/cd997f938b450010efa93aa8a65ecbed9a68a32e
I also verified behaviour was correct in both Firefox and Chrome. Updated CSS & JS was being loaded on extension manager page returned after the enable or disable action.