I'm seeing this too, though slightly differently than the two other ways described.
When I start X (on sid i386, with or without the alt_tab_fix.diff applied), whether from kdm or from "startx", the Alt key works normally in Emacs running as a separate X app, and Meta (i.e., "Windows" key) with tab works to switch windows in wmaker, but neither is recognized in an xterm (or "emacs -nw" from an xterm of course). I have found that I can work around this by holding down Alt and the windows key together; then I get the behavior I used to get from Alt alone. The windows key by itself doesn't do anything. The alt_tab_fix.diff did clear up the problem I was having in that each initial use of a modifier key was ignored. So Windows-L, which I have mapped in wmaker to open a local xterm, would be seen as an ordinary L the first time I tried it. The second time an thereafter it would open a new xterm as expected. The same thing for control and other modifier keys. This problem went away after applying alt_tab_fix.diff. I noticed this showing up perhaps a week ago. Thanks for your time, --Pete