I've seen the same thing during my experimenting with newtella. I've also seen the same thing, where connections seem to drop into something equivalent to "sleeping", just as you describe.

Every once in a while, they will auto-resume if I'm patient enough. I'm hardly EVER patient enough, though.

I'm wondering if this is a bug in the way that the client cycles among the active sockets for various communications -- searches, host connections, uploads, downloads. You know, if the client doesn't get "back around" to the download thread/socket in time, the remote client doesn't keep the pipe filled, and the connection sleeps/stalls.