Hi HomerJ,
I have seen this before where the version control flag gets stuck and doesn't change and report correctly as it should. Try the following:

I found that for some reason the value for the SF_IS_UNDER_VCS was changed. So in order to solve the issue please follow next steps:

1) Run a select query to verify if the SF_IS_UNDER_VCS value is in 'N'

SELECT SF_COLUMN_NAME, SF_IS_UNDER_VCS
FROM SYSTEM_FIELD
WHERE SF_COLUMN_NAME = 'TS_TYPE'

2) If the value is 'N', please run the update query below:

UPDATE SYSTEM_FIELD
SET SF_IS_UNDER_VCS = 'Y'
WHERE SF_COLUMN_NAME = 'TS_TYPE'

After this turn off the version control. Deactivate the project, and then reactivate the project and turn on the version control. The above values should then be correctly set and sticking in the system now and the error should not be occurring.

Try the above and see if this resolves your issue too.

Dan