Hate reading stories like this - have you both raised support tickets (via MySteinberg)…? How about supplying *.cpr files and/or the failing MIDI files for them to have a look at…?
One sure thing that will always hurt Cubase acceptance/adoption, is file incompatibility between different apps - ok, it can’t always be perfect; there’s bound to be some niggles. But you’re saying this is happening between versions of the same app…! Its not good enough and they should jump all over this, quick. Its just too easy for folk on the back of incidents like this, to say ‘oh, why don’t you just drop Cubase - its ****t. Get Logic instead…’ etc, etc…
And, anytime it turns out that Its not a Steinberg problem, there should be clear README’s or a Sticky posted about known file sharing/incomaptibilities (including between different apps).