Upgrade to 3.1 breaks custom data for a subtype

Might be related to CRM-5698.
If you have some existing custom data for, say, an activity of a certain type, then when you upgrade it no longer recognizes the custom data as being associated with the subtype. I.e. it doesn't display on the form, and when you go to edit the settings for the custom group it appears as though there is no subtype selected.
A look at the database fields in civicrm_custom_group indicates that it is now expecting the extends_entity_column_value to contain ascii 1's around the value, but in 3.0 there are no such characters present.