Hi David,
I've been working in SAP Support for years and never seen an issue like this. Are you sure that this is happening? When you right click on the DSO => Manage => Contents Tab => Active Table => Number of Entries you can see what the table contains.
You can do the same for the New Table.
How many Dataflows contain this DSO and how many Process Chain Variants contain this DSO. Perhaps there are functions/actions running on it from another process.
Anybody in your team have any code written to delete entries or move them?
Colm