Comment 24 for bug 1089804

I am sorry but the files you provided are exactly same!

And they look correct:

    key <AE01> {
        type[group2]= "THREE_LEVEL",
        symbols[Group1]= [ 1, exclam ],
        symbols[Group2]= [ 1, exclam, U05B1 ]
    };
    key <AE02> {
        type[group2]= "THREE_LEVEL",
        symbols[Group1]= [ 2, at ],
        symbols[Group2]= [ 2, at, U05B2 ]
    };
etc

So, keys 1 and 2 have proper mapping for both groups.

Try starting KDE or some other simple window manager, configure the keyboard and check. I guess GNOME does not use XKB for Hebrew.