[Thrashfinger]

Works with WoW v3.0.3:

The following code modification will resolve the "as intended" behavior which
currently (when items are equipped in both weapon slots) shows only the
equipped "off-hand" item for comparison if you hover over a "main hand" or
"two-hand" item.

Open the EquipCompare.lua file.

Change line 1237:
if ( itype == INVTYPE_WEAPON ) then

To:
if ( itype == INVTYPE_WEAPON ) or ( itype == INVTYPE_WEAPONMAINHAND ) then

This behavior (not bug) fix works, but with one noted side effect. After this
change is applied, "main hand" only items will be compared to equipped items
in both weapon slots, including "off-hand" only items and "one hand" items
equipped in the "off-hand" slot. However, "off-hand" only items will only be
compared to (if equipped) an "off-hand" slotted item. Although this may not be
perfect or ideal, I believe this quick and dirty fix (showing both items in
both weapon slots) is more user-friendly than the "as intended" behavior which
currently looks and feels more like a "bug" (based on user feedback here).

NOTE:
I do not know if this adversely affects other addons that have hooks for
EquipCompare. I use a small selection of addons and have not noticed any
conflicts.