Based on the information here http://www.ensembl.org/info/docs/api/core/core_schema.html#exon (click on Show columns), I believe this has to do with whether or not the stable_id for the exon has been changed. The description in the database schema is "Stable identifier version number". I believe that an increment of this version number means that the stable_id for this exon has been updated, perhaps due to additional evidence being provided for that exon, or a change being made to the transcript that warrants an exon stable_id change.

You could also check with the EnsEMBL developer mailing list via dev@ensembl.org OR helpdesk@ensembl.org.