The SanDisk Extreme arrived in the mail today. The linux image copied over easily from the old card to the new one. Sadly this didn't actually fix the problem. Talking to people on the PandaBoard irc channel it turns out that MMC has issues with reads and writes and I/O blocking. They recommended trying a usb drive for the main filesystem while booting of the SD card. The next post will be on the performance with an external drive of the OS.