UNC Espionage Probe

You can use omni-gel instead of playing the mini-game, you'll need 300 units of gel altogether. That aside, your experience with the timer does sound a bit peculiar, I don't recall it being unfair like that in either of my playthroughs.

That's very weird. My timer never runs while I'm doing the decryption. I basically have 10 seconds to move between the three bombs when not defusing them.

That;s got to be some sort of bug.  I'm sure my timer has always been at 9 seconds after Shep says his last line of dialogue and I can easily disarm all three using the mini-game even on Insanity level.  I would think you would be hard pressed to disarm all three even using omni-gel.  You've obviously reloaded after dying, but have you tried going back to a save before starting that mission and doing it over again from the start to see if it comes up the same way again?

Sounds like a bug.

Try to reload to an earlier save and see if it persists.