The first time it happened to me too, but then i loaded a save and ran straight on to the train.
Happened to me even when I didn't talk to the colonel (but I did kill the rogue offier). Kind of makes sense to take the deactivation code from his body, right? When I do that, the train blows no matter what way I defuse the bomb. The only way (for me) to complete the quest without a blown train was to let the rogue officer live and run straight to the train and deactivate the bomb. Any other scenario resulted in the train blowing up. Has to be a bug. I mean if you have already diffused the bomb why would it blow, right?