OSX has to guess which monitor is which, since the EDID info is the same for both (save the serial number, presumably, but OSX doesn't appear to pay attention to that). It usually tries to set things up to the previous setup by looking at how the devices are attached in the connection tree, however with Thunderbolt the connection tree isn't as simple as it was with displayport and USB.
You should be able resolve this by attaching one monitor at a time (ie, unplug the thunderbolt connection for the third monitor, attachthe second, then plug the third back in). However that's less than ideal, especially since all your apps will go back to the main monitor, rather than how you had them set up previously.
When Apple releases a refresh of the thunderbolt display, attaching one of the old ones and one of the new ones should also resolve the problem - they won't appear to be the "same" device, and so OSX will have an easier time keeping track of which is which.
Until that happens, another thing you can try is attaching the third one with a thunderbolt extension cable. It's an active device, and may alter the connection tree enough that OSX will have an easier time keeping track of it.
If that doesn't help, your best bet will be to wait until they refresh the thunderbolt display and upgrade only one of them when they do.