I've never had this problem before, but I do now. It's appearance has followed my recent update to the latest Adobe Premiere Pro CC 2018 update (Version 12.0.0, Build 224) and Adobe Media Encoder CC 2018 (Version 12.0, Build 202). Of course I'm not saying that these updates caused the problem, just making note of the timeline.
Here is what happens: I export a sequence from Premiere Pro using the File > Export > Media menu commands. Premiere Pro's Export Settings dialog opens, I select the Export Settings I want, then click on the Queue button. All seems to work normally, as Media Encoder opens, and I see the sequence listed in the Media Encoder Queue.
However, when I start encoding the queue, there is a flash of activity in Media Encoder's Encoding Panel, lasting maybe half a second, then the Encoding Panel goes blank and inactive, showing only the default words "Not Currently Encoding." A green check mark appears next to the sequence on the Queue, giving the appearance that it has been encoded.
But it isn't encoded. It could not have encoded in less than a second. When I navigate to the Output File, there is a file there with the title I requested for the video, however the File Properties show the video as having a duration of 00:00:00, and the video does not play.
If it helps any, here is a Dropbox link for a video, lasting 7 seconds, that shows what happens on Media Encoder when I click on the green arrow to start the queue.