Rant

[joebordes]

I just tried it and you and Andrea are correct: although you select the ContactID field to do the comparing it doesn't work if it isn't selected again in the mapping. I had never realized that, because I see no relation between the two concepts.
I will open a ticket and fix that, in the mean time, Andrea's solution is perfectly valid:
- create a custom field
- create an update workflow to copy the contactID to the custom field
- merge on the custom field
- eliminate custom field

I'll let you know when I fix the problem