Using EE 2.5.3 and MSM 2.1.4 on a local MAMP install
When creating a site with duplicate channel / duplicate entries it looks like copied data are left in the database alongside new data.
Bear with me, this is not easy to explain ;o)
If I copy channel data from site 1 to site 2 for a channel with only one custom field, I should only find the data in one column for each row in the exp_channel_data table for site 2. Not the case right now on my install.
What happens now is that, if I copy entries from site 1 using MSM and data are stored in column field_id_7 for example, when data are copied to site 2, I find a copy of entries data in field_id_37 but ALSO in field_id_7. Data in field_id_37 are updated (upload prefs) while data in field_id_7 seems to be a leftover from the copying and can / should be deleted. In fact I have deleted those data without noting any problem afterwards ...
Can you replicate the problem on your end? If that’s the case, I’ll go ahead and publish a bug report.