Currently, when you convert a project quote to a project the project ID will only be created for the auto-numbering segment if you have a multi segmented ID. In the test case, we had a 2 segment ID, first segment was a letter defined in a list of values for this segment, second segment is auto-numbered. When you click the convert to project button from the project quote, the project is created with only the auto-numbered segment, the first segment is blank.
If there is a validation of a segment value the system could return the list to properly populate the segment with validation during the convert to project process. The only work around for this is to change ID on every project you convert from a quote