I've had a similar problem before where Mr. Chicken let me re-check in, but for whatever reason spat out my outgoing BPs and the first segment of my return trip's BP, too. Even when checking in for the return trip, Mr. Chicken refused to give me anything more than that first BP, and when I tried to talk him into admitting he had more BPs for me, he spit out an error like the OP described.

When I finally got an agent's attention (those at SMF were seemingly ignoring the elite line, even though it was open), she spent a few minutes typing away before explaining that a "schedule change" had caused me to have to check in at the counter. No SSSS or anything (wouldn't have made sense, anyway, since I had my first BP to clear security anyway), but apparently the final segment had been dropped back 15 minutes. Very odd that that confused Mr. Easy so much!