From the trouble shooting forum over at XDA
Originally Posted by
redram38 
Are you saying that after I un-rooted the phone with RUU, applied the update, re-rooted the phone, if I put the MoDaCo Rom back on the MR update will not be there? If this is true then why is everyone doing this? I was under the impression once you got the update you could root the phone and put whatever Rom back on you wanted and still have the update.
That's right. If you apply the MoDaCo ROM you essentially undo the update.
This might be the problem for some of you losing your fixes