E39 Immobiliser issues... I think

Lads, do the Immobiliser or key/transponder give bother? The diagnostic scan showed an Immobiliser fault a couple of times but I passed no heed of it as the battery is a bit weak and I'd to charge it a few times after failing to start.
Over the weekend though , several times, it would fail to start, a court of times spinning and not firing, other times not spinning over, nothing happening in the "start" position.
When that happens, I had to remove the key, lock and unlock it, then it would go first touch.

Ideas?

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Are you using different keys? Sometimes the key(s) / car go out of sync - shouldn't happen that much, but it happens now and then with all of my E39's over the years - locking and unlocking with the key again resets it.

If the starter spins it isn't the immobiliser, as that is what the immobiliser inhibits.