pkall programmed again despite manual

Okay so something strange happened to me today. I was doing other work to my 4Runner and I disconnected the battery. Once I got finished I connected the battery. Then I tried to show off my remote start and my truck just cranked and cranked... I shut it down because I didn't want the starter to burn up... I tried it again with the key in and it worked. I had a feeling it was the bypass so I checked the connections (they all look good) Even though the manual says that they can't be programmed again, I figured I'd try it for the hell of it. Sure enough, I got 10 blinks on the LED... I'm thinking, wth... Is this common? This PKALL was programmed and working fine until I disconnected the battery. Did that cause it to lose it's mind?!?!

manual states after a battery disconnect must start with key once before remote starting