Spirit's communication problems put a damper on everything at work today. Although I think the media language is a bit extreme in this early stage, there's no doubt that there is a serious issue with the rover being in fault protection mode. I believe the mystery was primarily that the communication failure didn't totally match any of the branches of the fault tree, so there was some uncertainty why Spirit was doing what it was doing.
The question did come up in this morning's press briefing if a truncated command set could have caused problems, and the answer was no. Even with the bad weather at the DSN station in Canberra, if the connection was cut short, that shouldn't hurt our baby at all.