I've encountered this and also been baffled by it, and here's my theory.
Enterprise software is full of Java programmers. Like programmers of all stripes, many Java programmers are convinced that their language is the fastest, the most flexible and the easiest to use--they're not too familiar with other languages but are convinced that those who practice them must be savages and barbarians, because any enlightened person would, of course, use Java.
These people have built vast, complicated Java infrastructures: rube-goldberg machines of frameworks and auto-generated code full of byzantine inheritance structures and very, very large XML files.
So, when someone comes along and says "Hey! Let's use a C interpreted language! It's fast and has neat libraries and is much quicker for scripting and prototyping!" The Java guy is firstly like "I have to run a make file to configure this? QUEL HORREUR!" Then the reality of having to deploy and host this on servers that are running dated OSes and dated versions of Tomcat and nothing else starts to set in.
"Hey, I know! There's a java version of this interpreted language! It may break down in the fast lane on the bridge in rush-hour, and it sometimes catches on fire, but I can get Tomcat to run it. I don't have to dirty my hands with learning non-java stuff, and I can shoehorn it into the existing infrastructure! Win!"
So, is this the "right" reason for choosing a java implementation of a scripting language? Probably not. Depends on your definition of "right". But, I suspect that it's the reason they're chosen more often than snobs like me would like to believe.