I'm having similar-ish issues. Pure Fox layout with purple Zealios and LEDs. Used a Hakko soldering station set at 650 degrees F with 63/37 solder. I built the keyboard Wednesday morning, and everything seemed to be working fine. All the keys registered and all the LEDs worked.
When I started working this morning, I discover that the 4 and y keys aren't registering. LEDs for those keys are still lit. I swapped a new switch into the 4 key and still no joy. Y key spontaneously began working again. I figure I'll fart with it later in the day, but as the day goes on, I lose the y key again, the right shift stops working altogether, and the L key won't register when the right shift is pressed. All the LEDs still light up.
I flashed the board successfully two or three times last night and a couple of times today.
So, what gives? Bad soldering, broken trace(s), defective product? Some combination of the first two? Suggestions?