My guess would be that you are inadvertently hitting Command-X with all the regions of a track selected. If you're working on long pieces with lots of regions, it's a good idea to check the number of regions selected which shows in the upper left hand box on the arrange page (Logic 7) where the quantize, loop, transpose, etc. info is displayed. If you click on the track it will show how many regions there are selected, if you click on only one region in the track it will say 1 selected.