Assuming the OP installed all test pieces the same way, then are we looking something with the vinyl, adhesive, and substrate combination.
I think it's also probably safe to assume the original lettering done was done by the same installer, at the same time, with same technique (wet or dry), same squeegee, wouldn't you say? My guess would be two different brands of vinyl are why the black and red behaved differently.
Really interesting thread, for my backlits I use makrolon (polycarbonate), remove liners 24 hour before application (outward side only), install with rapid tac, and avery cast, never a problem yet. A customer of mine showed me a
sign that was done by someone else and full of tiny blisters. He asked me how is it possible that it happened, I had to tell him I have no idea. I think it's easy to say the installer messed up, had a bad squeegee, used wrong materials, but really do we know what they did wrong, if anything?