If the WHT has not been charged on Down payments you posted in Legacy, check the DP entry you are uploading. Suppose you are posting DP of 20000 INR with 2% WHT , then the entry should be like below,
Vendor A/C DR 20000
To Bank A/C 19600
To TDS on Rent A/C 400
Please check Vendor master - Withholding tax data for tax details
Thanks