Think I had the same issue as you - only a bit less complex setup. Only use one Outlook (2010), but with Exchange in the backend.
I experienced a lot of problems with this setup; tasks would for some reason get stuck and not update. My theory is that Outlook "versioned" the tasks after a sync issue with Exchange and MilkSync tries to sync a wrong version.
When this happens to a task, edits in Outlook is not reflected to RTM, and vice-versa.
I ended up with a one-time sync from Outlook -> RTM. To do this, I had to first export all to Excel, then "restore" in MilkSync, then reimport from Excel (losing most of my notes and the completion times of completed tasks).
Now I rely solely on the web GUI of RTM, I input from Outlook with e-mail (read up on Smart-Add, it's really smart!), and use the mobile app and iPad-friendly web gui.
MilkSync + Outlook (w/o Exchange) might be perfect.
However; IMHO, MilkSync + Outlook + Exchange is really not a robust/reliable solution.
Posted 3 years ago