To add to my quest:
Adobe QT32 server runs fine with After Effects CC 2014. When I export the same footage with AE to H264 it takes 1:28 . So maybe I should use after effects for encoding...
When I send the AE comp to Queue in Media Encoder it takes 3 min 32 to render is. That is in Media Encoder CC because Media Encoder CC 2014 can't open the composition ("comp is empty")