I use FogBugz for my job. I use Omnifocus for my sanity.
A long time ago I set up the included mail rule that comes with Omnifocus to route messages containing certain key phrases directly from mail into the task manager. Unfortunately it looks like every so often, Apple updates Mail.app; breaking the plugin that Omnifocus uses to route messages via the services menu.
Because the system had acted so reliably for so long; I didn’t notice when all of the sudden messages started disappearing from Mail. This had the potential to get me in to a lot of hot water so I went on a week long search for the cause.
As it turns out, the version of the mail rule that I was using from Omnifocus actually deletes the message from Mail.app during the routing. Unfortunately for me, the second half of the script that pushes the message in to Focus wasn’t happening because Mail had been upgraded in just such a way.
Deleting the mail rule manually seems to have corrected the issue, messages now remain in my inbox. Unfortunately for Omnifocus; I’m having to rethink my dependency on the tool.