I'm having this problem repeatedly when I try to use multiple instances of AErender.exe: I will be able to start a number of instances, and it will all work fine, but then something will snap and thereafter every time I try to start a new instance I see this: After effects error: Unable to obtain a license. Please run the full application to correct the problem or get a more detailed message.
As you can see I'm logged into CC, and After Effects is running, as well as several other instances of aerender.
The workaround is that I have to quit AE and then re-start it, which then brings up the CC sign-in dialog. It's really annoying to have to do this all the time. Just another symptom of the incredibly brittle nature of the CC sign-in system.
This is windows 7 Pro, 64 bit, latest CC version: 2015.3