Video transitions effect all layers

When I add certain video transitions to a track they seem to effect all the tracks beneath it. For instance, if I apply a checkerboard wipe to track 3 it will also do a checkerboard wipe on tracks 1 and 2 also...
Any thoughts?
Thanks in advance,
David.

Nope! Nothing selected underneath and it's not what should be happening. Will give you a bit more info...
The programme is a job opportunities slot:
On track one is a white matte.
On track two is our chromakeyed presenter.
On track three is a clip (resized to appx. 25% and rotated 90 degrees)which floats in the white space next to the presenter and provides an area to put up information about the job being discussed.
It is this resized clip that I have tried to introduce using the checkerboard wipe but when I apply it, it checkerboards all three tracks in from black. If I use a cross dissolve or some of the other transitions it works fine..?!
The other annoying thing is that it worked fine in an earlier version of the programme - could it be that this one particular sequence is corrupted somehow?
Have tried the same effect in other projects and it seems to be behaving itself...
Think I may have to pull in the boards that worked from the earlier version of the programme but it's annoying not knowing what's causing it.
Thanks for your replies,
David.

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