I am facing exactly the problem mentioned in these links:
http://code.google.com/p/android/issues/detail?id=2373
http://groups.google.com/group/android-developers/browse_thread/thread/2d88391190be3303?tvc=2
I have a simple root activity with the LAUNCHER and MAIN intents and nothing else. I start another activity with has no flags or anything extra in the manifest whatsoever.
I launch the app (root activity) and from there start the 2nd activity. On pressing the Home button the task goes to the background. On launching the app again (from Launcher or from holding the Home button for recent apps) it starts a new instance of the root activity on top of the existing stack.
If I press the back button, the new "root" activity closes and the old 2nd activity is visible, which means its launching the root activity in the same task instead of bring the task to the foreground.
To counter this I made the root activity's launch Mode singleTask. Now when I press home and launch the app again, it clears the activities above the old root task and brings the old root task to the foreground instead of just bringing the entire old task with the 2nd activity on top to the front. Note that the old root task still retains its application state, which means it wasn't a new instance, but the the higher activities had been killed.
It even occurs on other applications downloaded from the market. The manual install method has no effect for me, it still launches the same way.
This is due to the intents being used to start the app being different. Eclipse starts an app using an intent with no action and no category. The Launcher starts an app using an intent with android.intent.action.MAIN action and android.intent.category.LAUNCHER category. The installer starts an app with the android.intent.action.MAIN action and no category.
Whoever submitted the bug should have probably worded it as a request for enhancement to the Eclipse plugin since they apparently want Eclipse to have the ability to pretend to be the launcher and to start apps using the same intent as the launcher.