Another Key Fob issue

Well I checked the Forum search function but found nothing on this one. Up until the other day, my fob was working just fine. Then without warning, it quit working. Seeing this as a bad or dead key fob battery, I purchased new 2032 batteries and then replaced it. Still will not work.
So here is the story: With key in hand, will not start, I will get the single beep warning and amber key warning.
Hold key fob over start power button, same result. Tried cycling the smart key button under the steering wheel, still nothing. Odd thing here, when the push button is pressed in and attempt to start the car, it does nothing, no warning light no beep. The key fob red LED will flash when you attempt to use any of the 3 buttons on the remote but activates nothing. Holding the key fob over the power on button does nothing. Inserting the fob into the key slot the car will start and run fine, no unlocking the doors either with the remote or by grabbing the door handles. Also will not lock the doors using the external black button

 

Well that is all well and good, so I attempted to get another fob from Toyota and it was going to cost me almost $300 ($105 to diagnose the issue if it is the fob or the car, $149 for a new fob and up to additional $50 for any other services associated with the programing of the new fob if the old fob is toast). Ended up getting regular Toyota key cut from my VIN (free) and have just been plugging in the fob in the slot.

Yesterday, I got in my car after an extended time away and have been using the "manual" method since April and I sat and looked at my dash it wasn't blinking the key symbol so I thought,"give it a try", and the car turned on just like its supposed to and the auto entry and lock functions seem to be working again. I guess I should pick up another fob and try programing it. Any thoughts as to why the system seems to be "working"?