ImportGLJournal.java in iDempiere 3.1 at line 514 "Set Trxorg" sets the incorrect org. See below code:
// Set TrxOrg
sql = new StringBuilder ("UPDATE I_GLJournal i ")
.append("SET AD_OrgTrx_ID=(SELECT o.AD_Org_ID FROM AD_Org o")
.append(" WHERE o.Value=i.OrgValue AND o.IsSummary='N' AND i.AD_Client_ID=o.AD_Client_ID) ")
.append("WHERE AD_OrgTrx_ID IS NULL AND OrgTrxValue IS NOT NULL")
.append(" AND (C_ValidCombination_ID IS NULL OR C_ValidCombination_ID=0) AND I_IsImported<>'Y'").append (clientCheck);
no = DB.executeUpdate(sql.toString(), get_TrxName());
The bolded value should be OrgTrxValue.