This affects checkbox custom fields, not tested with multiple select fields but may affect those too.
When using the UI to edit the value of an option for such a field, the char_data field of relevant rows in the civicrm_custom_value table is updated accordingly, but only if there was only a single option selected.
E.g. I edited the value of an option from "9" to "09". char_data "9" was updated to "09", but char_data "2|5|9|12" (using "|" for [Ctrl-A]) was not updated.
Donald Lobo says this is not fixed by
CRM-1008, "Custom Checkbox and Multi-select Fields - Store and Handle Leading and Trailing Delimiter (Ctrl A)" and asked me to file this issue. See http://lists.civicrm.org/lists/arc/civicrm-dev/2006-07/msg00310.html