This happens due to a layer pagination state update bug in RenderLayer.
Created attachment 229876 [details]
Created attachment 229878 [details]
This patch makes the fast/multicol/multicol-with-child-renderLayer-for-input.html test pass also when run with region based columns enabled.
But wait a minute! I forgot to search for existing reports before filing this one, even if I knew that whatever worth filing for new multicol was probably already filed. Sorry about the mess. I'll close this one, and move over to bug 131808.
*** This bug has been marked as a duplicate of bug 131808 ***