I tested this on the demo.openngo.org/cicivrm site (drupal php5) and got the same as at home. Here's what I did:
1) Search for all individuals, export the first page of them.
2) Look for the one guy with "Dr" as a prefix, change it to "Dr." (I think it's Sam Adams) in the exported recs file.
3) Edit the name and email so it won't be a dup.
4) In CiviCRM administration, edit the "Dr" label so it reads "Dr."
5) import the exported records, including the prefix field. It will report an error in one row.
6) Download the records with errors and look at the one record: the prefix field contains "Dr" and not "Dr."
7) Go back and check the file you uploaded to be sure you changed it; yup, you did.
8) Go doublecheck that you changed the prefix label in CiviCRM administration: yup, still changed.
If periods aren't allowed in a label (or specifically a prefix label), that's ok but I couldn't find that in the docs anywhere. Sorry if I'm missing something obvious!