Hi Satish,
I don't think it's SAP standard behavior to dun negative balances.
Even in your scenario, the normal payments are not getting dunned.
Its only the SD refund line items which are going into dunning path.
Can you check, the dunning events thoroughly, event 300,311 in particular.
Also Check, if there is any thing done in the dunning grouping events,301,306 &309.
Check for any implicit enhancement as well.
Thanks,
Amlan