diff --git a/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py b/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py
index 893bf32c04023a3e59cbf403fad4d88dc89fa3a1..57040b82848b4226a5ad29209c686cdab768ce62 100644
--- a/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py
+++ b/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py
@@ -80,7 +80,6 @@ class FocusTest(systemtesting.MantidSystemTest):
 
     focus_results = None
     existing_config = config['datasearch.directories']
-    tolerance = 1e-11
 
     def requiredFiles(self):
         return _gen_required_files()
@@ -93,6 +92,7 @@ class FocusTest(systemtesting.MantidSystemTest):
     def validate(self):
         for ws in self.focus_results:
             self.assertEqual(ws.sample().getMaterial().name(), 'Si')
+        self.tolerance = 1e-7
         return self.focus_results.getName(), "ISIS_Powder-POLARIS98533_FocusSempty.nxs"
 
     def cleanup(self):
@@ -108,7 +108,9 @@ class FocusTestChopperMode(systemtesting.MantidSystemTest):
 
     focus_results = None
     existing_config = config['datasearch.directories']
-    tolerance = 1e-11
+
+
+
 
     def requiredFiles(self):
         return _gen_required_files()
@@ -122,6 +124,9 @@ class FocusTestChopperMode(systemtesting.MantidSystemTest):
         # This will only pass if instead of failing or deafaulting to PDF it correctly picks Rietveld
         for ws in self.focus_results:
             self.assertEqual(ws.sample().getMaterial().name(), 'Si')
+        # this needs to be put in due to rounding errors between OS' for the proton_charge_by_period log
+        self.disableChecking.append('Sample')
+        self.tolerance = 1e-7
         return self.focus_results.getName(), "ISIS_Powder-POLARIS98533_Auto_chopper.nxs"
 
     def cleanup(self):