Launching multiple instances of the After Effects aerender application on one computer in that way has never been a tested or supported workflow. If it worked, it was a happy accident.
Dang. A VERY nice accident. Expedited render times.
Should a put this in feature request?
... though we think that what we have in store for next year will make such little hacks seem silly. (We have a large portion of our team working on some projects that should make folks like you who want faster rendering very happy.)