Changes made to the Environment Variables are not remembered if changed from the textfield.
You have to press the ... button and edit the variables from the table.

Steps:

• Click "Run">"Edit Configurations..."
• Add a new configuration
• In the "Environment Variables", enter "a=1"
• Press the "..." button
  => The table is empty. It should contain "a | 1".
• Cancel the Environment Variables dialog
• Press OK on the "Run/Debug Configuration" dialog (in Environment Variables should still see "a=1")
• Click Run>Edit Configurations...
• Select the configuration you had created
  => "Environment Variables" is empty. Should be "a=1"