Thanks Chris.
Well, it was not functionally fine in reality, because it crashed (*).
Your comment helped, in the sense that it attracted my attention on a stupid bug: NewTrackExtraList_->at(track_counter) should be NewTrackExtraList_->back(), because track_counter is valid only within this function while NewTrackExtraList_ has a larger scope.
However, the problem persists:

<pre>
----- Begin Fatal Exception 02-Apr-2014 11:16:34 CEST-----------------------
An exception of category 'InvalidReference' occurred while
   [0] Processing run: 1 lumi: 1 event: 1
   [1] Running path 'simulation_step'
   [2] Calling event method for module MixingModule/'mix'
Exception Message:
Inconsistency RefCore::pushBackItem: Ref or Ptr is inconsistent with RefVector (PtrVector)id = (1:184) should be (1:165)
----- End Fatal Exception -------------------------------------------------
</pre>

Any hint of what else I can try?

(*) To do a test, you need to edit the last line in FastSimulation/Configuration/python/CommonInputs_cff.py from GenMixing to DigiRecoMixing, and then execute /afs/cern.ch/user/g/giamman/public/test.py