When I run System Info from Tools Menu the information it provides is not up to date - wrong version of MT, states modules missing when in fact they are installed.
When I run mt-check.cgi it provides the correct information.
Seems like MT is not using mt-check.cgi but something internal; the address bar displays "mt.cgi?__mode=tools" when I run System Info.
Any answers?

The information on the System Info screen is cached for 24 hours. If you're making changes right now, your best bet is to just use mt-check directly, as no simple way of dumping the cache is provided. You can do it with an SQL query(which I don't have handy), but I don't see much point in it myself.
Thanks Su. Odd way of caching especially without documenting.
There's been no real response as to why it's being done or if the request to kill it will be fulfilled. If you want to add your disagreement, please comment on that bug.
You can clear the cached version of the System Info page with the following SQL query:
delete from mt_session where session_id="SC"