If you run the report named "System Specification - Left Aligned", it will fill in the sequence numbers.  That report generates the squence each time it runs, so if anything changes, it still has the correct order.

I'm having a similar problem, only with an existing project (in 2.3.4)

Some of my items don't have sequence numbers at all. Editing and/or moving the items don't create a sequnce number for that item. I've even tried moving from the folder to another. New items seem to get a valid sequence number, new folders don't.

In reports, some items that have been moved from one folder to another show up under the old folder with a sequence number belonging to the new folder (this is without 'Sort' selected for the report - selecting 'Sort' just makes things worse).

Some items have the same sequence number.

See attached image from a partial report.

Kevin, see my response to Alessandro above.  You have to run an "SRS" report in Contour.  When you do that, Contour will look at the order of all items and folders in the set you just ran it on, and sequence them accordingly.  If you change the sequence in any set, you have to run an SRS report for that set to get rid of NULL values, and disordered items.