SKS and key fob not working, it's not a 12v battery problem.

Hi all,
I am a longtime reader of priuschat, but I have never run into an issue requiring a special post before. As stated in the title, I am having an issue with the SKS system and key fobs, also potentially the 12V system.
The car is a 2005 tide lands pearl with SKS, leather and the sound package. I have owned it since 25k miles, and it just turned 200k, so I am a member of that club. Before I bought the car, it had been in a front end accident but no electronics were harmed. Also to date, I have done no major work on the car. The 12V battery was initially changed in 2011 with an optima yellow top.
The recent issue started when I mistakenly drained the optima 12V battery, requiring a jump. Following the jump that, night the car behaved fine. Then I drove about two hours to Redding, CA where the car would not lock with SKS, and the dash showed the flashing yellow key with exclamation mark and the car emitted three beeps when I walked away from the car with the fob in my pocket.
Using the car meter, I checked the 12V battery voltage and it showed 11.8 to 11.9 resting with the car in ACC mode. Reading on the forums, I drove home about 3 hours and replaced the battery with a new small 400 CCA12V battery for a lawnmower as the shop did not have the proper prius 12V battery.
That night after a 25 min drive the car locked with SKS and all was normal
The next morning and all following days the car SKS has not worked, the yellow key and exclamation mark flashes when I close the doors and walk away with the key, even if the trunk is open. I checked the ACC voltage again and it read 11.9 as before, so I thought maybe the small battery I bought was not strong enough. I took it back to the store at which point both it and the original yellow top in the back of the shop measured 12.55 volts with a multimeter. I don't understand why the car reads .5 to .6 volts lower than the actual battery open circuit voltage.

I then tried a fancy 18Ah lithium polymer battery which had a measured open voltage of 13.22, and upon mounting it in the car had a voltage of 12.4 on ACC mode. I also replaced the key fob battery (I have only ever had one). The key fob/yellow light was still an issue, so this is not a 12v battery issue that I can tell.
I ended up buying the $200 SuperStart AGM prius battery and then I drove from Oakland to LA (about 6 hours). Upon arriving in LA, the car measured the new AGM battery at 12.0 or 11.9V in ACC mode, and the smart key issue remained. In IG-ON mode, the car reads 13.8 to 14.2 volts.
Also this morning in LA, it appeared the trip meter and clock reset at some point before I started driving this morning.

I can lock the car only manually when the SKS button is off and I use the physical key to turn the lock, but I think there is a larger issue at work and I really need to figure it out before I get into a tight spot, so please help!
There are no MIL lights on the dash.
Is there anything else you need to know, and what should I do next?

 

All, thanks for your responses.
RE; battery connections: when I replaced the battery, the new one has JIS sized posts, so they are a bit smaller than standard US posts. I have used some braided ground cable fill the gap between the JIS posts and the standard battery connectors. The connections are pretty tight.

Yesterday I checked the night time voltage with a multimeter to be 12.6 volts. Yesterday morning it was 12.2. I don't know if this means there is a phantom draw. The car reads the voltage half a volt lower. The smart cancel button is engaged at night as the smart key system as the smart key/ key lock/unlock did not work, and the yellow key flashes if I don't turn it off.

I have replaced the batteries in my one key, twice. Te original and replacement battery voltages were measured to be 3.0 and 3.1 respectively. The red light flashes when I push buttons.
My original keyfob was pretty beat up so I thought maybe the smart key was broken. Also, I had a newer used fob I bought from ebay a few years ago, so I used the chicken dance procedure to program the immobilizer, then I used techstream to do a seed reset with purchased key codes. However, it seems the smart keys cannot be programmed because the smart key system is off due to some issue, which again may be battery related.
Now I have 2 used fobs that work in the ingition slot, but none that unlock doors or are smart in any fashion, even in the car.
There are no errors in techstream and no error lights on the dashboard.
Any other thoughts?

Thanks,
Orion

 

I love to be proven wrong.
I ran the car for a bit in ON mode and it charged the aux battery to 12.6 volts, or 12.2 as the car read it. Then I tried techstream smart key registration again and I was able to register the new and the old smart key!
So now I have 2 smart keys that do nothing smart outside the car, but don't have to be in the ignition slot within the car.
Ie, the original problem remains; The smart key will not lock or unlock doors, and the yellow key symbol lights up on the dash when leaving the car with both smart keys.

Thanks much,
Orion

 

Update: I believe I have found the cause of my issues. I unplugged a phone battery pack and the charger in the 12v port in the center console. At that time, (when the car was off, I noticed that the charger light remained on.

I have had no issues with the SKS system since, so perhaps the car will not operate the sks if something is charging when the car is "off".

In fact I have the kit to adapt the original small battery terminals to standard US sizes, but I don't know if the original japanese battery terminal sizes can be purchased. Any ideas on this?

Thanks for all the input.