In AFJ we filter incoming HTTP requests based on the content-type header. It seems that aries-toolbox does not include any header, meaning the message won't be handled in AFJ.
I've removed the restriction for content-type in my clone of AFJ and that seems to work. We should send the content-type header when sending DIDComm messages over HTTP:
We accept both the old and new one:
V0 = 'application/ssi-agent-wire'
V1 = 'application/didcomm-envelope-enc'