I've never had any real issues with Media Encoder, but in the last few months, it is just not rendering what I send to it.
My main workaround was just saving my AE file as a new name - but it was a pain and soon started to not help. I found sometimes deleting the tmp files in the AME folder and purging AE worked...but again a lot of hoops to jump through that soon didn't seem to make a difference
I recently updated AE and ME from Adobe to see if that would help, and still, it won't render. It just hangs on "Connecting to Dynamic Link" and eventually fails.