Keyfob or SKS system

Have 2007 Prius 3 with keyless entry/start. Recently I had an issue with the fob not working so I installed brand new battery and still nothing. Checked both batteries and they both were reading accurate voltage readings. I went to Toyota and it was going to cost me almost $300 to have the system troubleshot and new fob purchased and programed. I opted to have a key made from the VIN and have been just using the key to open the doors and plug the fob in to start. then the other day I forgot to pull out my fob and the door unlocked and the keyless start worked. The next day it reverted back to using the key and plugging in the fob. About two days ago, it started working again.
What could be causing this? Do I need to get another fob and program it when it is working? I could really use some help (and no I do not have another fob)

 

Thank you. I will take a look at the aux battery. The fob has started working again and has for the past two weeks.

 

I had a new key cut from the VIN which Toyota (my local dealer) made or me free of charge. It was easier to have a full size key on my key ring then trying to keep pulling lut the fob key. thn using thefob inserted in the key slot to start the engine. As I mentioned, the ystem has started working again. I will be checking my aux battery to see if that is potentiall

UPDATE:
So I started to have the issue again with the fob not working and requiring to insert it in the key slot. I left for work about a month ago, left my car with my fiance and told her to drive it as she needed to. Seems the day before I am to come home, she went in to start the car and nothing, dark would not do anything. After getting home I too looked at what was going on. Seems the screen was totally dark so that meant I had lost the AUX battery. What a joy that was gettin that battery out. Put it on a 2 amp trickle charge for about 6-8hours. Put back in and drove about 40 miles to local AutoZone to have it checked, they checked it in place and said that the battery was at about 86%. Still driving the car but have to insert the keyfob.

Found the Diagnositc check and did that. Static voltage is 12.0 VDC, headlights on drops to 11.7. Another interesting issue has ocurred now, my drivers window controls ... the window will not go up or down in auto mode (where you push the button fully and the window goes up or down totally). Do not undertand what is going on.

While the battery appears to be an OEM Toyota battery I have no idea how old it is. Any further things I can do to check this battery. I hate havin to spend $200+ for a new battery if I don't need to. Really can use some input here