There was a patch I stumbled onto within the Chromium OS repository that might help with this; it seems to have been removed after they actually patched it into Chrome itself. Not sure what happened with the QA for the patch or if it was sent upstream or not.
links here: X: Map Alt-Up and Alt-Down to Page Up and Page Down
The patch is as follows:
This is a probably-wrong fix for an issue where autorepeat
is disabled for keys assigned by XKB. As far as I can tell,
XKB has the correct autorepeat settings for the keys before
a completely-empty autorepeat array from X is copied over
it; then the XKB array is copied back to X. This makes us
skip the first copy.
diff --git a/xkb/xkbUtils.c b/xkb/xkbUtils.c
index 75e243c..bceb55c 100644
--- a/xkb/xkbUtils.c
+++ b/xkb/xkbUtils.c
@@ -342,9 +342,6 @@ CARD8 * repeat;
xkb= xkbi->desc;
repeat= xkb->ctrls->per_key_repeat;
- if (pXDev->kbdfeed)
- memcpy(repeat,pXDev->kbdfeed->ctrl.autoRepeats,32);
-
XkbUpdateDescActions(xkb,first,num,changes);
if ((pXDev->kbdfeed)&&
I've yet to try it myself, but will probably take a shot at it in a bit.