Does it lag in time, or are they of varied luminance and one is lighter than the other so it appears to last longer? You might consider assigning both to a parent and let the parent do the wipe if it's not a luminance issue.
Depending on the speed of your processor, you could be seeing a reduced frame rate (i.e. not 30 fps) preview. Try doing a ram render (Shift-B) of the clip and see if it works the way it's supposed to.