I have the exact same problem on the following configuration:
Windows 7 Professional (64-bit)
Eclipse JEE 3.7.1 (Indigo) (64-bit)
JBoss 4.0.3SP1
JBoss Tools 3.3.0 M3 (also tried the nightly builds)
I haven't found the solution yet. On the one hand, you can use JAR and give it a ".war" extension. There's really no fundamental difference between the two. On the other hand, I don't know what functionality I'm missing because I haven't gotten to try the WAR option to see what it does.