Using 'Switch with Source Schema' option returns different results (4335414)

When comparing two schemes and using the 'Switch with Source Schema', the results sometimes differ from the original run.

Steps to reproduce the problems (note that this only happens under some circumstances)

1. Go to Database | compare | Schemes
2. Go to "Target Schemes and Output" section and select another schema there
3. Click on the green arrow to start comparison
4. Once it finishes,r-click the target schema in the "Target Schemes and Output" tab and select  "switch with Source Schema"
5. Click the green arrow