Victor,
You are correct - the Get Converted Leads Auto Synch should clear the Lead ID. I would check two things - did the record run through the Auto Synch correctly? If so, I would check to see if the record exists as both a Lead and a Contact in SFDC - there could have been duplicate lead records, the non-converted lead could have been modified to trigger it in the Get Leads Auto Synch, etc...
Best,
Kristin