There are a few differences between the '98 ( the one I know the most about) and the '99-'00's.
I'm still digging through some VADIS info, but I think
you have an anti-theft system that's
pretty much the same as the '98 along with an additional layer of starting protection.
It sounds a lot like there's something wonky with the basic Anti-Theft system.
The basic Anti-Theft is the alarm that's part of the central locking system.
It watchs doors, hatch and hood and triggers flashing parking lights and the
single horn mounted high on the firewall. It prevents the starter from engaging.
That module (2/76) contains the central locking "brain" and door lock motor relays.
It gets keyfob signals from the remote receiver module ( 4/19 ) mounted above the
instrument cluster. There are also some optional tilt and glass breakage sensors.
Those seem to be pretty rare in most markets, but are shown in the diagrams.
The "next layer" is the chipped key reader. They call it the "Electronic Starter Inhibitor".
To me, that seems rather misleading, as it's function appears to be allowing the starter
to engage and let the engine turn over, but cutting fuel flow and preventing the engine
from actually starting.
Using an antenna ring that surrounds the ignition switch, the system reads the chip
embedded in the key head and determines if you have an authorized key or not.
( Many owners with this system have had issues with the connector contacts at the
antenna ring getting oxidized and causing "It turns over, runs for a second, then quits"
syndrome. Some have had success with unplugging and reconnecting the antenna ring
connector a few times to wipe the contacts and solve that problem.)
The diagrams here will show you just how many fuses are involved in these systems.
In your situation, I would scribble down all the fuses involved and start metering.
Rather than just pulling the fuses and looking at them, use a meter to check
voltage while they're in the fuse box. You should see the same voltage at each
of the nibs on top of each fuse. That way, you KNOW. Keep in mind that the
key will have to be on for a couple of these.
Again, I'm making some assumptions here, but
hopefully, it may help get you on the right track.