Why's that? It's a numbers game, says Polytron. The patch fixes multiple issues with the game (including framerating and loading problems, death loops, and more), and the save corruption issue affects less than one percent of players overall. Because sending out another patch to fix the first patch would cost Polytron "tens of thousands of dollars" to get the game re-certified by Microsoft, the patch is coming back, and any players thus affected by the save issue will just have to deal with it.
Polytron points to this as a major drawback with Microsoft's Xbox Live Arcade service, in that the company charges exorbitant fees to developers to release even free updates and content. "Had Fez been released on Steam instead of XBLA," posts Polytron, "the game would have been fixed two weeks after release, at no cost to us." Does that mean a Steam version is in progress? "Only a few months left to our XBLA exclusivity!" says the company on Twitter.