If your question is: "Why did someone who isn't available to answer install Java 1.3 on one of our Progress 9.1E servers when we have Java 1.4 running just fine on all the rest (that also run Progress 9.1E)?" then the answer is: "I don't know."
If the question is: "Why do the Progress 9.1E installation instructions specify Java 1.3?" then the answer is probably "Because Progress version 9.1E is a revision of Progress 9.1 which was first released almost 10 years ago when Java 1.3 was on the cutting edge."
If the question is: "Will Java 1.4 work with Progress 9.1E?" then the answer is: "Probably, it seems to be working with your other installs and, so far as I can remember it has always worked for me. But, as Casper pointed out, Progress is sometimes very picky about the Java API and a previously unknown problem could occur. On the other hand it doesn't sound like you are using the components of Progress which are especially sensitive to Java version."
If the question is something else you'll have to clarify and we can try to help. But keep in mind that Progress 9 is ancient, obsolete and almost completely unsupported (9.1E is sort of "supported") and that we are mostly responding from memory not from having live production systems that we can whip off a test case on.