Are you sure they're timed improperly? I've ripped a lot of stuff with subtitles and not once have I had subs improperly timed.
What I have had are subs that don't display properly timed in Windows Media Center and Windows Media Player but do properly display in VLC and XBMC. I don't think this is because the subs are ripped incorrectly via MakeMKV but probably something to do with which filter or splitter you have handling thew subs in the Windows players. I haven't experimented enough with FFDShow and Haali to see which would yield the better results in WMP/WMC but considering thsoe two players are the only ones I have issues with I'm betting it's them and not the actual file MakeMKV spits out, especially considering the damn hoops required just to get those players to play a MKV file in 64bit Windows.