Trash your AE Preferences. Double-check that you have AE version 11.0.4. If not, get it.
If you're rendering with After effects directly, try switching to Adobe Media encoder. It works much faster and has many more output options.
This is kind of a weird symptom you have here but is it really bogging down render time? The issue itself, not sure but since it would render one at a time had you purposely placed two things in the render queue, presumably in the end there would also be two output files with one finishing before the other. I'm curious if you ended up with two files?
Still having problems? Let us know.