I had the exact same issue as you! It's an issue only in the newest version (JUNE 2017) [06-2017] of the form. This is what I noticed:
When you fill in the form for the first time and you validate, it validates successfully and the box changes to Yes. And then you save it, it stays as Yes. BUT if you close it and open it after saving, it says No, and if you click validate again, despite saying validation successful, it stays at No and never changes to Yes.
What I did was, I filled it out, validated it, it said Yes, I saved it and just uploaded it without opening. I'm hoping that will be okay. The thing is, if it isn't validated properly, it shows red boxes around the errors, and actually doesn't let you save anyway. So the fact that your submission shows no red boxes means it's validated, hopefully that should be enough for IRCC. Since there's no barcodes, it's not too big of a deal. Fingers crossed when they open it it says Yes.
So far they haven't rejected it. I'm May 16 too, I uploaded it on June 12 (same day I got AOR). Background check still says Not applicable on my MyCIC account but if it changes to in process that means they accepted it and there's no issue. I'd love to bring this to their attention though.