Steps to reproduce:

• Create a simple test project
• Create a second, "Custom Executable" Run config (set it to run "ls -lach" for instance)
• Quit and Start Qt Creator again
• Re-open the project, check that "Run Settings" still points to the Custom executable
• Change the active run setting to the actual binary
• Quit and Start Qt Creator again
• Re-open the project
• Check which Run Setting is selected

Expected:

• The actual binary is selected

Actual:

• The Custom executable is selected

Seems to be a side effect of the Target / Build / Run Settings refactoring as the ActiveRunConfiguration is now stored twice as well, but I gave up investigating at that point.