Thanks for reproducing, and for trying to find a workaround. This is my first InfoPath project (I'm a general computer consultant), so I thought maybe this behavior has a purpose of which I am unaware. But it seems wrong to me, and I was surprised to not find anything relevant via Google search - I figured someone else would've tried something similar.
My solution was to get all other aspects of the Repeating Table and fields, Drop Downs, etc. dialed in, set the background color I wanted in the table which encloses the Repeating Table, THEN insert a fresh Repeating Table, drag all my fields into position, delete the original, "damaged" Repeating Table, THEN set the Conditional Formatting for shading the repeating rows when the Checkbox is unchecked. Knowing this limitation/bug, planning ahead will prevent the double effort in the future.
I've never reported a bug to MS, and all I can find is Microsoft Connect: http://connect.microsoft.com/directory/accepting-bugs, and it appears they are not accepting bugs for InfoPath.
Thanks again.