Yes, Jira is the place to go for bug reports. I am also not too sure what version of Java you are running, but I am not too sure if Jira is doing any bug fixes anymore on the 2.x line, but I think they might be doing a few more. Most fixes are being fed into Java 8. Also are you using the beta Scene Builder, or the public one? Also check Jira in the top right "search" to see if this issue has been asked before, because it's a good possibility, and they are very good about helping out with issues.
Lastly you might not even have an issue, so what exactly happens? You get a NullPointer in Scene Builder itself? There might be an issue in your Netbeans code(since it can be displayed with issues) whereas you might be getting a random error which Scene Builder isnt' liking...