Could you please also show:

setxkbmap -layout us -option misc:typo -print

xprop -root | grep XKB

Here it is:

$ setxkbmap -layout us -option misc:typo -print
xkb_keymap {
	xkb_keycodes  { include "evdev+aliases(qwerty)"	};
	xkb_types     { include "complete"	};
	xkb_compat    { include "complete+ledscroll(group_lock)"	};
	xkb_symbols   { include "pc+us+inet(evdev)+group(shifts_toggle)+level3(ralt_switch)+compose(rwin)+nbsp(level3)+srvr_ctrl(terminate_ctrl_alt_bksp)"	};
	xkb_geometry  { include "pc(pc104)"	};
};

and

$ xprop -root | grep XKB
_XKB_RULES_NAMES_BACKUP(STRING) = "evdev", "evdev", "us", "", "terminate:ctrl_alt_bksp,grp:shifts_toggle,grp_led:scroll"
_XKB_RULES_NAMES(STRING) = "evdev", "evdev", "us,ru", "altgr-intl,typewriter", "grp:shifts_toggle,grp_led:scroll,nbsp:level3,compose:rwin,terminate:ctrl_alt_bksp,misc:typo,lv3:ralt_switch"

this is "default" properties, that were selected from gnome dialog. Here is misc:typo present, but not in "setxkbmap -print".

That is odd - the xkb option misc:typo does not enable symbols/misc(typo) section. 

Could you please also attach rules/base file?

Thanks

Created attachment 29726 [details]
rules/base

Here is rules/base file.

Very strange... With your (and same with mine!) rules, I am getting this:

$ setxkbmap -print -model evdev -layout us,ru -variant altgr-intl,typewriter -option '' -option grp:shifts_toggle,grp_led:scroll,nbsp:level3,compose:rwin,terminate:ctrl_alt_bksp,misc:typo,lv3:ralt_switch
xkb_keymap {
	xkb_keycodes  { include "evdev+aliases(qwerty)"	};
	xkb_types     { include "complete"	};
	xkb_compat    { include "complete+ledscroll(group_lock)"	};
	xkb_symbols   { include "pc+us(altgr-intl)+ru(typewriter):2+inet(evdev)+group(shifts_toggle)+level3(ralt_switch)+compose(rwin)+nbsp(level3)+terminate(ctrl_alt_bksp)+typo(base):1+typo(base):2"	};
	xkb_geometry  { include "pc(pc104)"	};
};

Could something be broken in your X (xmodmap, libxkbfile, ...)?

I'm sure that it is installed correctly. It could be a bug in one of X components.
I have following versions installed:

no xmodmap
libxkbfile-1.0.4
xorg-x11-xkb-utils-7.4
xorg-x11-server-Xorg-1.6.99.901

(In reply to comment #6)
> no xmodmap
Sure there is xmodmap, in xorg-x11-server-utils-7.4 package.

libxkbfile1 1.0.5-1ubuntu2
x11-xkb-utils 7.4+1ubuntu2

and xkeyboard-config from git.

Actually, would you try xk-c from git? It should not really matter, but just in case...

Tried xkeyboard-config-1.7 and libxkbfile-1.0.5 and it works the same.
Also filled bug in redhat's bugzilla, but I doubt they will look or fix it soon https://bugzilla.redhat.com/show_bug.cgi?id=524919

Any other ideas what could be broken?

If you apply the patch from here:

http://bugs.freedesktop.org/show_bug.cgi?id=16975

 to setxkbmap, you might get explanation of the rules setxkbmap applies

Created attachment 29961 [details]
debug output

Here is debug output from:
$ setxkbmap -v 10 -model evdev -layout us,ru -option '' -option misc:typo -print

I see it matches misc:typo rules:

The rule from group 22.  Option(s): "misc:typo" in the rule, requested "misc:typo":   Layout[1]: "*" in the rule, requested "us": wildcard.  The rule is to apply later.
The rule from group 23.  Option(s): "grp:alts_toggle" in the rule, requested "misc:typo": ignore.
The rule from group 23.  Option(s): "misc:typo" in the rule, requested "misc:typo":   Layout[2]: "*" in the rule, requested "ru": wildcard.  The rule is to apply later.
The rule from group 24.  Option(s): "grp:alts_toggle" in the rule, requested "misc:typo": ignore.

But there is no block of "Applying the deferred rule" at the end. Could you attach your output for the same command to compare (or diff right away)?

That's what it is!

http://cgit.freedesktop.org/xorg/lib/libxkbfile/commit/?id=e695be2ab7eb1361b204f98c3da872eff58ad6b5

*** This bug has been marked as a duplicate of bug 19563 ***

Yay! It fixed issue. Seems, libxkbfile deserves new release :)