Assumptions:
1) Drive letter case should not matter on Windows platforms
2) The location of the JRE should not matter.

Problem:
If you have a captive JRE in a subdirectory of your application and invoke the
application with a command that specifies the jdkhome directory with an
uppercase letter, i.e. 

c:\myDir\ide\bin\myApp –jdkhome C:\myDir\jre

the splash screen appears followed by an error dialog with the following text:
Warning - could not install some modules:
        Actions APIs - No module providing the capability
org.openide.modules.ModuleFormat1 could be found.
        Actions APIs - The module Dialogs API would also need to be installed.
        Actions APIs - The module Explorer And Property Sheet API would also
need to be installed. . .

With NetBeans 5.5, you get the option to Disable and Continue but it does not
work, of course – the application is hopelessly hung and the process tree has to
be killed manually.  In 5.0, it just hangs.

If you invoke the same command except that the jdkhome is specified with a
lowercase c:, it works.

------------------------
Steps To Reproduce:
------------------------
1. Build a zip distribution for the Feedreader sample and extract it to c:. 
This creates c:\feedreader.
2. Copy a jre into this directory.
3. Execute this command (make sure to use an uppercase drive letter):
feedreader\bin\feedreader --userdir user1 --jdkhome C:\feedreader\jre
and you will see the splash screen followed by the error dialog.
4. Replace the uppercase jdkhome drive letter with a lowercase one and it will work.

--------
Analysis:
--------
In ModuleSystem.loadBootModules(), the value of the variable manifestUrlS always
has an uppercase drive letter.
IF the jre drive letter is also uppercase, the “startsWith” clause is matched,
so the MANIFESTS: loop continues and some critical components are not processed.
 Specifically, these boot modules are NOT loaded:
org.netbeans.bootstrap
org.openide.modules  
org.openide.util
org.netbeans.core.startup
org.openide.filesystems


This was first reported in netbeans forum thread in August 2005:
http://www.netbeans.org/servlets/BrowseList?list=nbdev&by=thread&from=206393

I’ve seen it from time to time, but have been unable to create simple steps to
reproduce until now.  I’m still not 100% sure of the cause or solution, but
believe it to be at least reproducible now.  It’s a really nasty bug because it
stops you cold and the solution (changing the drive letter) isn’t obvious or
intuitive, but once you discover it, the solution is simple enough that you
don't want to waste any more time debugging it.  I hope there's enough
information here that it can be fixed.