Rx300 Problems With Keys / Immobiliser

[LexusRX300]

Hello!

I purchased a repossessed '99 Lexus RX300 from the local bank. It has a blown engine & didn't come with any keys.

I took the ECU out and sent to a locksmith to get replacement keys cut and the ECU reflashed.

It is supposed to come back in Auto Key Mode, but it does not appear to be in that mode. Here is what's happening:

With no key inserted, the security blinks slowly: blink...........blink..........blink

When a key is inserted, but not turned on, the security light blinks rapidly three-four times and then a pause: blink.blink.blink.............blink.blink.blink.................blink.blink.blink

When the ignition is turned on, the security light goes back to blinking slowly.

What problem does the above indicate? How can I correct it? I don't know if the ECU will let the engine run or not as the engine in the vehicle is seized and I have not had the new engine installed yet.

Thanks in advance!