MR2 for BES 4.1.6 has been release by RIM. We've had it a while, but it only went public yesterday. It has a fix for MDS-IS and MDS-CS servers running in distributed environment. Other fixes are also included that maybe pertinent to your install, particularly some memory leak issues have been addressed with HTML emails. See the release notes here.

Get it from the BlackBerry site.

FYI, STS is not yet running MR2 (probably later this week), so be sure to test before you go to production.