Setup:
NetBeans 6.5 RC2
Sun (Apple) JDK 1.6.0_07
Mac OS X Leopard (10.5.5)
NetBeans-bundled JRuby 1.1.4
Rails 2.1.0


Beginning with "Tools -> Servers -> GlassFish v3 Prelude -> Jruby -> Deploy All Rails Applications At Root Context (/)"
turned on, and my application (twittertracks) running at "/", I perform the following steps.

1) Shut down the GlassFish server by clicking the "Stop the Server (X)" button next to its output pane.
2) Change the root context setting to off.
3) Start the GlassFish server back up either by right-clicking on the project and choosing "Run", or via the "Services" pane
4) Observe in the server output: 

INFO: Jruby version is: 1.1.4
INFO: Starting Rails instances
INFO: New instance created in 13,495 milliseconds
INFO: Loading Rails application twittertracks at /
INFO: Loading twittertracks Application done is 14084 ms

Expected: The application should not have been loaded at the root context. It should have deployed at /twittertracks.
NetBeans then sends the browser to http://localhost:8080/twittertracks/, and a Rails routing error is returned because
the application is not there.

5) Stop the server again, the same way as shown above.
6) Start the server again, by right-clicking on the app and choosing "Run".
7) Observe in the server output:

INFO: Jruby version is: 1.1.4
INFO: Starting Rails instances
INFO: New instance created in 13,359 milliseconds
INFO: Loading Rails application twittertracks at /twittertracks
INFO: Loading twittertracks Application done is 13927 ms

It has gotten it right on the second try. The application is now loaded where it should be.

This next set of steps is slightly different, and demonstrates another aspect of the problem.

8) Change the "root context" setting mentioned at the outset back to on without first stopping the server.
9) Right-click on the application and choose "Run".
10) Observe: The application is not redeployed at "/" as is expected. The browser is sent to http://localhost:8080/ and
finds a GlassFish welcome page there, instead of the Rails application. The Rails application is still available at
http://localhost:8080/twittertracks/
11) Repeat steps 9 and 10 as often as you like. (In the attached log, I ran through them only once more before continuing.)
12) Stop the server.
13) Start the server (right-click and "Run" application)
14) Observe in server log:

INFO: Jruby version is: 1.1.4
INFO: Starting Rails instances
INFO: New instance created in 12,980 milliseconds
INFO: Loading Rails application twittertracks at /
INFO: Loading twittertracks Application done is 13705 ms

It has now correctly loaded the application at the root context, in accordance with the setting changed in step 8. 

Attached is the messages.log file I generated by running through all of the above steps after starting NetBeans from the
command line, passing it -J-Dglassfish.level=FINE