Are you sure the structure is dry? Sometimes the water permeates through the carpet and underlay, hits dust and other biological items and promotes bacteria and mould growth. You can't see it from the surface but the odour is present. In this instance, cleaning the carpet without removing the biological load or fully drying the area, may actually make matters worse.
I suggest you either lift the carpet and underlay and inspect underneath, or use a penatrative moisture meter to check.
Hope this helps,if not give me a call.
Regards,
Chris