Workaround is to explicitly add
require 'myjar.jar' to the file.
Fixed in 8776e6b8f1bf. Note that with more than one jar in the classpath this still doesn't work with JRuby 1.4.0 due to http://jira.codehaus.org/browse/JRUBY-4265. It works when running since in that case the IDE can use the -classpath switch, but the debugger has to set the classpath through the CLASSPATH env variable.
Integrated into 'main-golden', will be available in build *201003240200* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
User: Erno Mononen <email@example.com>
Log: #179364 - Classpath not set correctly when debugging