Hi Sairam,
Check on below points,
1. Are you displaying same set of fields in MultiProvider as in query.
2. Check your query for any conditions.
3. Is your query has characteristic (hierarchy) drilled down.
If hierarchy is drilled down, make it as flat list and compare the records. There are chances of sub nodes data aggregating into top node and inturn records will be more in query.
4. Check the Total/Sum of the all records between query and MP.
5. Restrict your query for a day or week and then compare. Idea is to make records set small and compare whether report is wrong OR your MP selection wrong ;-)
Hope it gives way to find the difference.
Thanks,
Umashankar