I've observed that whenever the shell inserts an integer, whether it be by using a $set or an $inc in an update, or by inserting a new document, the integer gets stored in Mongo as a double. This becomes a problem when you're using the new $bit modifier as it doesn't work with doubles. I've narrowed the problem down to the Shell rather than a deeper problem, as 1.2.4 of the Ruby driver doesn't exhibit this problem.

As a side issue, I'd suggest having the Shell displays doubles as such, e.g. with a trailing ".0" such as "5.0" instead of just 5. This would make it more obvious to identify such problems as this one in the future. It's only through Ruby that I can actually see that the integers being inserted by the Shell are actually doubles.