So I ran into this problem recently. The issue was in the build/run configuration. Apparently android studio had chosen an activity in my project as the launch activity thus disregarding my choice in the manifest file.
Click on the module name just to the left of the run button and click on "Edit configurations..." Now make sure "Launch default Activity" is selected.
The funny thing when I got this error was that I could still launch the app with from the device and it starts with the preferred Activity. But launching from the IDE seemed impossible.