This is basically it. When your application has not been used after some time, App Engine will swap it until another request appears.
When this happens, it downloads all the JAR applications that your application requires, which can take a very long time, in some cases, 10-15 + seconds.
I have no experience with JRuby in particular, but this page contains some tips on how to reduce application startup time. Tips should be useful even if you are not strictly writing vanilla Java.
Basically, just don't include JARs in which your application is not heavily dependent.
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