I played "Failure to Communicate" under 2.2c last night with no problems, except for the objective of defending the science cruiser... that is very nearly impossible. I did what I did before, and extracted the mission, opened it in FRED2, and gave the cruiser a ship-guardian sexp. Personally, I think that you should swap the Phoenix (or Treb or whatever you've given the Nephilim) for the Shivan light bomb... something that the player has a chance to shoot down.
On another note, as was mentioned in the SCP and other sub-forums, I encountered a problem when playing the mission in subspace under HT&L. The subspace effects were there for less than a second, then they vanished entirely. I played the rest of the mission just fine, but the subspace effects never returned. While I'm talking about it, that must have been the easiest time I've ever had in that mission. I was using the default difficulty level and we took down the Lucifer with more than 5 minutes to spare, and I didn't lose a single ship. Either its a change in the mission design, or it was the fact that I gave all of the Ulysses advanced disruptor cannons.