Masupra,
I had a little trouble like you describe after I had to have my door handle replaced.
Dealer did it, but the locks never seemed to quite be right again after, until I fixed it.
Not exactly sure what I did that fixed it, however. I've been into the door quite a bit and each time fiddle with it to see if I could make a difference.
But, I'm of the thinking that at the time the connections are made, both doors need to be in the same state. That is, if you connect the driver door lock in an unlocked position when the passenger door is locked, they get out of sync.
The other thing which may help and not require going in, is to cycle through all the lock/unlock possibilities for each door and by every means a couple of times to get them sync'd up.
That would be power unlock driver, power lock driver, manual lock driver, manual unlock driver, use the handle pull to force lock the driver door from the outside when closing. Then, do it all for the passenger side. Repeat a couple of times. The passenger side power lock will also lock the driver door and stay locked when the door is closed from the outside, unlike the driver door (unless the handle pull technique is used).
Anyway, you get the idea. Get them coordinated. Then, test the security. Keep an eye on the security light setting as you work. Wait for it to blink when you expect it should.
Just a thought. Let us know if it works for you.