I just upgraded a server to 4.0.3644.2 from 4.0.3573.2. We have set up a scheduled task that runs a series of run profiles. Now one of my two AD management agents will run fine for two cycles and then subsequent cycles see a stopped-server on delta sync. Looking at the event log, I see that miiserver.exe is crashing on a 0xc0000005 (access denied) exception on either ntdll.dll or clr.dll.
If the service auto recovers, it doesn't fix the issue, however, if I manually restart the fim service, the next 2 cycles again are good, followed by an indefinite number of stopped-server/crash runs. This environment is set up with the same rules extensions and supplementary custom components as 3 other environments that I've upgraded, but this particular environment and this particular MA is the only one that I'm seeing this behavior on. I've run full imports and full syncs on the MA, with no improvement. I moved to 4.0.3684.2 with again no improvement.
For right now, I've put a restart-service command in the ps1 that runs the full sync, however, this is a stop-gap only and cannot be a long term solution. I cannot upgrade to R2 at this time, but will be doing so in about 6 months, so that is not an option at this time.