In 4.1, steps to reproduce:
1. Right Click a Project and click properties
2. Right Click project and click run
The project properties become disabled during the run (expected), but when the run is complete they never re-enable. You have to close the properties and re-open them again.
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This is a known issue in 4.1.0 and will be fixed with the upcoming service release. Thank you for reporting this problem, though!