Android Studio installs old code / doesn't restart application despite instant run is OFF

Question

I'm using the new Android Studio 2.0 (Beta 6) and I'm facing a serious problem. After updating, I noticed that there were some problems with the Instant Run feature, where it was quite hard to ensure that the application was actually running new code. I disabled the Instant Run feature immediately.

Despite this, I am noticing that Android Studio does not always deploy new code anyway!

I have tested my theory by adding a print when my Activity is created and it doesn't get called. If I close the application (for example by pressing the back button) and then running the code - it works as expected.

I have also verified that it's actually a problem, since old code is run after pressing the run button.

What the F is going on and does anyone know a fix? (Except reinstalling AS 1.5)

Notes and summary:

• There is no lightning bolt on the Run Button
• Activity onCreate Print is not called after pressing run
• Changed code is not updated after pressing run
• Instant Run is turned off in Preferences (And restart activities on code change is on)
• It doesn't happen every time - roughly 50 % of runs