JBuilder, since version 3.5, is an application 100% pure java. So it can work with any OS wich has an implementation of a JVM. I've not tried JBuilder 5, but since now, the only problem met with JBuilder was with Windows 9x: using the IDE sometime the screen glitches, but it can be fixed uncommenting following line inside JBuilder4injdk.config to disable direct draw:

#vmparam -Dsun.java2d.noddraw

As Windows ME is "directly derived" from Windows 9x I believe this could be an inherited issue, but I don't think JBuilder can have further problems with Windows ME.