I noticed earlier today that as of 1.1, the Blizzard maps were updated from v0.1 to v1.0. (Agria Valley is currently at v1.2.) Also, in the SC2 Editor, some Blizzard maps are showing up as not downloaded:
I haven't played 3v3 since pre-1.1, so all the updated 3v3 maps are still marked as Not Downloaded.
This supports Mag Roader's theoryMag Roader's theory that the downloads consist of map data.
So, here's what I think it is: When you join the matchmaking queue, the game asks Battle.net for a list of maps you might about to be playing on. If you have the latest versions of all the maps, this will probably only take a second.
If any maps are out of date, however, the game will update them. This will take a few seconds for each map since they're around a megabyte each.
This system would let Blizzard publish updated versions of maps, or add new ones to matchmaking, between actual patches.