99LB (the German version) has the baloons getting released and the generals deciding to treat it as an opportunity for a show of force blowing them up intentionally.
99RB, on the other hand, has the EWS confusing them with a threat causing the system itself being the source of the attack.
The message between songs is different, the German version is a warning about the wrong people being in charge of the doomsday machine whereas the English version is a condemnation of the doomsday machine itself.
Interestingly the band was not satisfied with the English version, mainly because they wanted to be a pop band and not a protest band and they thought the English version was too "on the nose" in its condemnation of MAD.
Personally I grew up hearing 99LB on the radio but thinking about the lyrics of 99RB since I don't speak German. 99LB was more popular even in the english speaking world because it's better performed but we all saw it as an anti-MAD protest song which 99RB definitely is, but 99LB is not quite.
99RB has some really great lines missing from 99LB:
The war machine springs to life
Opens up one eager eye
and Call the troops out in a hurry
This is what we've waited for
This is it boys, this is war