please check whether the feild status of your document types KZ, KA and KG are having the status for WBS Elements as optional or hidded WBSE field check at the vendor-recon account.
On enabling the WBS element field in the field status variant, it solved your purpose but the point to ponder is that if the WBS field may be suppressed then why did it allowed WBS to populate when doing payments through F110. Maybe raise this with SAP same point.........