Need remote gone wild

Well.. I hope some folks are still out there after the Control4 buyout...

Here goes... After about 24months, about 3-4 weeks ago, my remote started acting bizarrely.  I would turn on Apple TV or Tivo, and every 2min or so , the apple TV would exit program being watched, and navigate erratically. Similarly, when watching Tivo, every so often the channels would change 20-40 times, then stop for 1-2min.

If I use the remote control app in my iPhone, all the problems go away. The system functions normally!

Setup includes:

1. Neeo remote v 0.53.8-d91faab1

2. Tivo / Apple TV / Onkyo BR Disc / Denon AVR-X2200W

4. An IR remote control extender.

I have vetted the IR extender by testing with a completelyu new one. I have even gone as far as purchasing a secondhand Neeo system, thinking that perhaps the kids dropped the old remote. SAME thing happens with the alternate remote & brain (Old brain & remote replaced completely).... and yes I like the system that much...

Still, the iOs app makes everything function perfectly!

I feel like I am being gas-lighted. 

Any thoughts on why this is happening? Was there an update to the remote around 6/1? (Which would be bizarre given the Control4 buyout.)

Completely confused. Thanks for any input or thoughts.