Hi Thomas,
Can you check your mds.ini if the item "Distribution Root" contains the correct path?
Couple of things that I noticed in the past are that inconsistencies might arise when you change an import-map or syndication-map (referenced by an automated port), without restarting the MDIS or MDSS. Also, manually 
changing the port-folders will cause issues.
Anything like this occurred maybe?
Kind regards,
Gerwin