Product Version: NetBeans IDE 6.5 (Build 200811051154)
Java: 1.6.0_07; Java HotSpot(TM) Client VM 10.0-b23
System: SunOS version 5.11 running on x86; UTF-8; en_US (nb)

Not 100% reproducible.
Steps to reproduce:
- start profiling CPU session of AnagramGame
- in Live Results window right-click com.toy.anagrams.ui.Anagrams.guessedWordActionPerformed(java.awt.event.ActionEvent)
 and select Add to Instrumentation roots...
- stop profiling session
- start profiling CPU session of AnagramGame with the following options: Part of Application
- click "edit..." link
- invoke Add From Project button. Open nodes of the Projects tree to AnagramGame | Sources | com | toy | anagrams | ui |
Anagrams | Methods and check checkbox for nextTrialActionPerformed(java.awt.event.ActionEvent) method
- click OK
You'll see now Selected Root Methods list is empty (see screenshot). It is not 100% reproducible. And if you click OK
button of Specify Root Method dialog, you'll see on Select Profiling Task dialog there is text '2 root method' next to
Part of Application radio button.
So it seems that functionality works well, but data are not visible sometimes.
This is also reproducible with Web Application: when switching to "Default Package View" the list is empty sometimes
(http://qa.netbeans.org/modules/profiler/promo-h/profiler60.html#web_project_6 step 3).