I don't know if this is related, but it might be, and I'd hate to withhold evidence.

The other day, I was transferring a ridiculously large file (a little over 220MB) from the empeg using the FTP daemon. It transferred it in a reasonable amount of time with no apparent pauses, but then, when I went back to play some more at the serial console, where the player had already been stopped (via `q') and I had been playing at the bash prompt for some time before the FTP started, there was no response to serial input. I let it sit there without doing anything more to it (as I was dealing with the file I had just downloaded and didn't feel like debugging the new problem yet), and it eventually came back. I didn't time it, but it seemed to be about 20 minutes.

Again, I don't see how this could be related, but the symptoms seem awfully similar. There was nothing going on on the empeg besides the bash prompt idling and the FTP daemon pushing all that data and whatever other processes exist all of the time.

(Edit: I should point out that I'm using an ancient version of HiJack -- v200.)