Then trouble was a Russian communications device was down onboard the station (the FGB MDM2), and it would take 3 orbits to fix.
They had to use the Moscow Ground Stations to talk to the station instead and you can only do that when you are flying over Russia. They had to power down the space station before the astronauts on the spacewalk connected the power cables!
 

EGILS (electrical systems) Flight Controller at work

There was also a problem that sent the shuttle into free drift and so they had to reconfigure the Digital Auto Pilot.  I think it was a problem with the Vernier jets being down.  Then they had an RCS Jet failure right after that.

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