Are your LD's the same as the US LD's, if so there should be NO problem at all cutting right at the end of 1 scene and going right into the next, I to have the '97 SE Trilogy on LD(it is a big box set) and I have no problems butting the 2 right up to each other, video and audio.
can you post an sample of what you are doing with the side changes? something sounds a little strange to me, this should not even be an issue, unless the PAL set is really weirdly done.