If you have multiple copies of the same application on your hard disk, it can be a bit unpredictable which one will launch if you say
tell application "MyApp" to activate
Here is a code snippet I figured out for making sure it is the one in the /Applications directory that gets launched.
set mypath to ""
tell application "Finder" to set mypath to path to the "apps" from system domain as string
set mypath to mypath & "MyApp.app"
tell application mypath to activate