One quick question, how are these orders entered into the system? Manual entry, import with VI, EDI?

These that are displayed are imported through Insynch, I deleted one order and reentered manually to see if it would fix itself and the order I entered manually did not show in the "on SO" field either.

in certain circumstances the qty on sales order field is not updated as it is with manual entry so you have to rebuild the sorts almost daily. That is how it is with VI, might be same with Insynch 

Haven't had an issue until a couple weeks ago since we upgraded in March, all data looked correct from March-Sept., nothing major changed.  We added Sage Alerts, some queries to pull data from PO Header/Details, added some scripts to SO Header/Details, I can't think of anything else.

Removed a script I added and then rebuilt sort files, assuming since this script touches the warehouse table it could be the culprit.  Not sure I understand why it would through numbers off that aren't even being affected by it though.

'table pre-totals need to make sure boxes are unchecked'
'If oSession.CompanyCode = "TST" then

	If oBusObj.EditState = 2 then

	sType = ""
	nCustomerNo = ""
	cNewHire = ""
	dRushDate = ""
	sCCheckBox = ""
	sVendorNa = ""
	sShiptext = ""
	searchString = "picked up"

	rVal = oBusObj.GetValue("OrderType$", sType)
	r=oScript.DebugPrint("OrderType: " & sType)

		If sType = "S" then

		rVal = oBusObj.GetValue("CustomerNo$", nCustomerNo)
	
			If nCustomerNo <> "2922000" and nCustomerNo <> "2668000" and nCustomerNo <> "2672000" and nCustomerNo <> "1096000" and nCustomerNo <> "0801000" and nCustomerNo <> "2517002" and nCustomerNo <> "1657000" and nCustomerNo <> 			"1942004" and nCustomerNo <> "3068000" and nCustomerNo <> "3079000" then
								
			rVal = oBusObj.GetValue("UDF_SHIPPINGMESSAGE$", sShiptext)
			r=oScript.DebugPrint("UDF_SHIPPINGMESSAGE: " & sShiptext)

				If Instr(UCase(sShiptext), UCase(searchString)) =0 then
	
				'rVal = oBusObj.GetValue("UDF_NEWHIRE$", cNewHire)
				'r=oScript.DebugPrint("UDF_NEWHIRE: " & cNewHire)

					'If cNewHire = "N" then

					rVal = oBusObj.GetValue("UDF_NEEDDATE$", dRushDate)
					r=oScript.DebugPrint("UDF_NEEDDATE:" & dRushDate)

						If dRushDate = "" then

						Set oLines = oSession.AsObject(oBusObj.Lines)
						r=oScript.DebugPrint("After AsObject oSOLines ")
						rVal = oLines.MoveFirst()
						r=oScript.DebugPrint("After MoveFirst ")
						Do Until cBool(oLines.EOF) 'Keep looping until record pointer is on last line'

						rVal = oLines.GetValue("UDF_CCHECKBOX$", sCCheckBox)
						r=oScript.DebugPrint("UDF_CCHECKBOX:" & sCCheckBox)
					
							If sCCheckbox = "N" then

							rVal = oLines.GetValue("UDF_VENDOR_NAME$", sVendorNa)
							r=oScript.DebugPrint("UDF_VENDOR_NAME:" & sVendorNa)				
								
								If sVendorNa = "LAPCO MFG. INC." then

								rVal = oLines.SetValue("WarehouseCode$", "009")
								rVal = oLines.SetValue("APDivisionNo$", "00")
								rVal = oLines.SetValue("VendorNo$","0001226")
								rVal = oBusObj.SetValue("UDF_ALLOCATED$","N")
								rVal = oBusObj.SetValue("UDF_DATE_ALLOCATED$","")
								rVal = oBusObj.SetValue("UDF_DATE_PRODUCTION_RECEIVED$","")	
								rVal = oLines.SetValue("UDF_CCHECKBOX$", "Y")
								rVal = oLines.Write()						
						
								End if
							End if
						rVal = oLines.MoveNext()
						Loop
						'End if
					End if
				End if
			End if
		End if
	End if
'End if

Are the lines marked as Drop Ship?  Are the line items for the same warehouse?

The lines that are getting changed by the script are not drop ship lines.  On the SO we could possibly have multiple lines for the same warehouse but after the script runs it could change 1 line to the "other" warehouse.