diff --git a/erpnext/hr/doctype/payroll_entry/payroll_entry.py b/erpnext/hr/doctype/payroll_entry/payroll_entry.py
index 4d008fc8296..7104c5f1eef 100644
--- a/erpnext/hr/doctype/payroll_entry/payroll_entry.py
+++ b/erpnext/hr/doctype/payroll_entry/payroll_entry.py
@@ -33,7 +33,7 @@ class PayrollEntry(Document):
 		if self.payroll_frequency:
 			condition = """and payroll_frequency = '%(payroll_frequency)s'"""% {"payroll_frequency": self.payroll_frequency}
 
-		sal_struct = frappe.db.sql("""
+		sal_struct = frappe.db.sql_list("""
 				select
 					name from `tabSalary Structure`
 				where
@@ -54,7 +54,8 @@ class PayrollEntry(Document):
 				where
 					t1.name = t2.employee
 					and t2.docstatus = 1
-			%s order by t2.from_date desc"""% cond, {"sal_struct": sal_struct, "from_date": self.start_date}, as_dict=True)
+			%s order by t2.from_date desc
+			""" % cond, {"sal_struct": tuple(sal_struct), "from_date": self.start_date}, as_dict=True)
 			return emp_list
 
 	def fill_employee_details(self):
diff --git a/erpnext/patches/v11_0/create_salary_structure_assignments.py b/erpnext/patches/v11_0/create_salary_structure_assignments.py
index b5ee6c6a291..712269ae6de 100644
--- a/erpnext/patches/v11_0/create_salary_structure_assignments.py
+++ b/erpnext/patches/v11_0/create_salary_structure_assignments.py
@@ -8,9 +8,15 @@ from erpnext.hr.doctype.salary_structure_assignment.salary_structure_assignment
 
 def execute():
 	frappe.reload_doc("hr", "doctype", "salary_structure_assignment")
+	frappe.db.sql("""
+		delete from `tabSalary Structure Assignment`
+		where salary_structure in (select name from `tabSalary Structure` where is_active='No' or docstatus!=1)
+	""")
 	for d in frappe.db.sql("""
-		select sse.*, ss.company from `tabSalary Structure Employee` sse, `tabSalary Structure` ss
-		where ss.name = sse.parent AND sse.employee in (select name from `tabEmployee` where ifNull(status, '') != 'Left')""", as_dict=1):
+		select sse.*, ss.company
+		from `tabSalary Structure Employee` sse, `tabSalary Structure` ss
+		where ss.name = sse.parent AND ss.is_active='Yes'
+		AND sse.employee in (select name from `tabEmployee` where ifNull(status, '') != 'Left')""", as_dict=1):
 		try:
 			s = frappe.new_doc("Salary Structure Assignment")
 			s.employee = d.employee
diff --git a/erpnext/patches/v11_0/move_item_defaults_to_child_table_for_multicompany.py b/erpnext/patches/v11_0/move_item_defaults_to_child_table_for_multicompany.py
index 4fd677a7373..390f42740bd 100644
--- a/erpnext/patches/v11_0/move_item_defaults_to_child_table_for_multicompany.py
+++ b/erpnext/patches/v11_0/move_item_defaults_to_child_table_for_multicompany.py
@@ -11,10 +11,12 @@ def execute():
 	[ default_warehouse, buying_cost_center, expense_account, selling_cost_center, income_account ]
 
 	'''
+	if not frappe.db.has_column('Item', 'default_warehouse'):
+		return
 
 	frappe.reload_doc('stock', 'doctype', 'item_default')
 	frappe.reload_doc('stock', 'doctype', 'item')
-
+	
 	companies = frappe.get_all("Company")
 	if len(companies) == 1:
 		frappe.db.sql('''