First of all, Paolini was still at the front of the bunch with 1km to go. Then half of the peloton was held up by a fall (of an Argos Shimano guy), so they have to check who was still in that group at 3k. Nothing to do with Italian time keeping.
Regardless of whether he has or hasn't lost time again today, I still don't think it's a good sign that Wiggins went missing again in the final 3km.
He was well placed around 4km, sitting at the front of the bunch with 2 team mates around him, and then once the sprint teams started to move things on he disappeared. Henao was still around the front, and Uran seemed to be a bit further back but Wiggins must have dropped right back to the last wheels.
I know he might be worried about pile ups, but hanging off the back of the bunch on his own, whilst other GC contenders and his own team mates are much further forward seems an odd tactic, especially after what happened yesterday.