Thank you everyone for the informative responses. Since reading this feedback I have been trying to watch more closely what triggers the message to popup, and you are all correct. Rezzing a prim on a "floor" has triggered it, as well as moving various objects. No big deal in and of itself, however I am also noticing a major hit to region performance when this happens.
As soon as the message for rebake triggers, the regions time dilation, FPS, and physics FPS fluctuate heavily. I will keep an eye out and see if I can pinpoint other reasons for this, as I'm not sure it's not a coincidence with teleports in and out quite yet. What I do know, the message isn't going away at all unless the rebake is performed, and once the rebake is performed the region performance returns to normal.
As I said, I will continue my observations since there are any number of things that could be happening at the same time and post back here if I find any other correlations. Thanks again for the help!