SH3 Commander could have sabotage and malfuntion feature applied to your game. If that is not the case then I suggest you undo step-by-step the mods in the JSGME list. That's the only way to find out what makes the hypdropone fail.
[EDIT] Damn I should read posts better before I respond. Yes, this looks like the sabotage/malfunction feature and waveheight being 'stuck'. Make sure you roll-back SH3 Commander after shutting down the game. I suggest you enable the auto-roll-back feature, so SH3 Commander does that automatically. Also, starting the game from within SH3 Commander is better imho, rather than starting the game with the usual shortcut.
Last edited by Pisces; 11-17-12 at 08:29 AM.
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