Most tissue based toilet rolls are actually made from two layers of tissue. It is a common problem for these two layers to become detached. From this the out of phase toilet roll problem can occur. The two layers become out of phase in their orbit of the cardboard tube and the perforations in the two layers of tissue are not lined up. This can be very annoying.

The two layers generally look something like this (sorry for the ascii art diagrams):
(1) -------------.-------------.
(2) -----.-------------.-------------.
(. = perforations)

The solution to this is actually quite simple. Keeping the lower layer stationary, pull the upper layer around the back of the roll - in effect, swapping the two layers. Having done this, you will find the (now) lower layer is slightly longer than the (now) upper layer from having gone round the tube an extra time. However, the perforations almost always now line up:

(2) -----.-------------.-------------.
(1) -----.-------------.-------------.-------------.-------------.

Having done this you can simply tear off the excess tissue:

(2) -----.-------------.-------------.
(1) -----.-------------.-------------.

If you wind the top layer round again they once again go out of sync. I think this is how the problem must originate. Toilet rolls are fairly tightly rolled together so I dont think think they could simply slide out of phase.