Rebooting does not clear this problem, in fact, I went into the Samsung specialist at my local Best Buy store (where I purchased the case) and he wasn't able to fix it either. My case was still under warranty but I don't have the original packaging for it (likely tucked away in a moving box).
He suspected something to do with NFC, but troubleshooting those settings also didnt resolve.
Also, the phone does register when it is in the case, as I have options to match theme colors to the case, and options to edit the led icons -- and it operates as expected with a clear-vue type case.
The phone has been rebooted several times, cache cleared, etc - and I am up to date on all software and security as well.