Ok, I finally figured it out, thought I don't think this could have been made more complicated if they tried. You're right that installing the Java Updates through netbeans (using the repository) placed the 2012_v48 in my cRio_Images folder. Now, when I try and re-image the cRio, I get:
Unable to complete operation because of unexpected error:
Error -2147220304 occurred at nisyscfg.lvlib:Restart.vi:1
What is causing that? I noticed that my cRio Imaging tool is numbered Version 2001.11.18. I installed the two updates from:
http://joule.ni.com/nidu/cds/view/p/id/2262
http://joule.ni.com/nidu/cds/view/p/id/2263
but the version number hasn't changed. What's going on?