The repair ships could be "very special" repair ships.  

This too has happened in the past: cut a cable, and then "fix it" very well indeed.  

Alternately, this could be "traffic forcing," whereby the Iranian government, cut off from normal comms, will have to use its backup routes: the ones that are normally only used in emergencies.  Thereby disclosing those routes and making them future targets for interception or attack.

I smell a major SIGINT collection effort in this one, and to my mind that's the only explanation that makes sense of all the facts.  

To that, add this:

A few years ago, a high-level Bushie leaked to one of Ahmed Chalabi's guys that the US had succesfully broken Iran's high-level military & diplomatic encryption.  The very next day, NSA intercepted a phone call from the US to Iran, informing the Iranian government of this fact.  No one was ever prosecuted, though it would have been easy to determine the source of the leak (if anyone's interested, I can spell out exactly how this would have been done).  

This was widely reported at the time, though its significance was not reported.  It was hugely significant:  an act of treason in high places, and an enormous loss for US intel.  

If in fact the present outages are part of a major collection attempt, then we can also infer that NSA has been unable to break the upgraded encryption systems Iran would certainly have put into use after the leak.  Thus they're going for the "brute force attack," for which they've determined that capturing all the traffic is necessary.  

Anyone have a better hypothesis, I'm all ears.  In a manner of speaking:-)