Have you talked with NI about that? I was debating whether that was worth for me to investigate further. I have learned to let a few versions go before upgrading and the thought of having to recommend using a RTE I haven't tested thoroughly (or even superficially) just for my app to be functional is not too exciting. Where is this written that checking that box meant you HAD to use the LATEST RTE? This sounds like a bug.
I've encountered a black imaq image display in exes, solved by unchecking the box to allow running in a later runtime version. Don't know if that is related to your problem.