I discovered that if you use an aggregate such as count(*) where you don't reference a specific column, the xml that is generated is missing the required tags.
There are tags for <ColumnReference><column></column></ColumnReference> that must be between the <mapping_text> and the <Data_type> tags in the xml that is generated. The table and column referenced in the aggregate function are placed there, but if you use a * as you would in sql the tags are not generated.
It will work fine in IS but is skipped when you import into another project.
I know there are some other known issues with exporting and importing projects expected to be resolved in the next service pack, perhaps this will be resolved too.