E46 immobiliser query!

Guys I had something peculiar happen to me on Friday night. I parked at Clearwater Mall as normal. About 2 hours later when I jumped in, the car refused to start.
Everything worked, the radio, lights, air con, hazards, windows, etc. I could arm and disarm the car but it just would not swing.

Not even the dead battery "click,click" sound. I managed to roll it out it the intention to kick start, but it refused to kick start.

This led me to believe that it could have something to do with the alarm/immobiliser.

After playing with the key, I closed the sunroof, and suddenly it started

I just don't know what it could be

If the batteries were low in the key, would it not have prevented me from disarming the car?

I used the car yesterday morning, and there was no problem.

At lunch time today when I tried to start it, it refused again

So I immediately tried the spare key, and it started

So maybe there is a problem with the original key?

Or is there something else majorly wrong?

Can the system be overidden somehow?

My concern is that I'm driving down to Durban on Friday morning and can't afford to get stuck.

It's not like it will kick start

Anyone else has something similar happen to them on the E46.

Pleas help...