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If you are on R12, please apply the patches in these two docs and check then.
iSetup: Imported Transaction Types Using iSetup Populates ORG_ID Value In Legal Entity Field [ID 1340427.1]
R12.1: Loading Payables Option Extract into Target Fails with the Following Exception: java.lang.NullPointerException [ID 1323037.1]
Also, make sure you have all the recommended patches applied.
Isetup List Of Mandatory Patches For R12 [ID 811040.1]
iSetup Mandatory Patches post 12.1.1 [ID 857551.1]
iSetup Mandatory Patches for 188.8.131.52 [ID 1317257.1]
184.108.40.206 isetup mandatory patches [ID 1337228.1]