Logged for future reference. I hit this problem today whilst finishing up a solution for a client using the B3401200.F3460EditLineAndUpdate JDE business function which has a right justified 12 character szF3460Branch parameter. Initially within my map I applied simple padding logic to the field. JDE threw errors related to invalid business unit so I theorized the JDE adapter was removing my padding. After googling around a bit I found this link, http://msdn.microsoft.com/en-us/library/aa559202.aspx.
I simply added B3401200.F3460EditLineAndUpdate.szF3460Branch to C:\Program Files (x86)\Microsoft BizTalk Adapters for Enterprise Applications\J.D. Edwards EnterpriseOne(r)\Config\jdearglist.txt, then regenerated my schema for the business function, and everything worked nicely.