In premiere pro 2.0 I added white mattes (1 frame every other frame) to a clip to make it look like the clip was flickering. When I imported the clip into AE it didn't recognize the black and white effect I used in PP2.0. I posted about that earlier. Due to my footage being widescreen I used motion/scale in PP2.0 to scale the white frames to keep the white matte of of the black bar areas on the top and bottom of the frame (widescreen letterbox bars). Upon import into AE the motion/scaling I didn't in PP2.0 was ignored. The white matte covers the whole frame. I tried to fix this (not too familiar with AE yet) by dragging the box/wire frame in the monitor window. This worked, it scaled the white matte, but it did it to a number of my clips as well (not all). How can I scale the white matte clips and not the footage?
Probably you simply accidentally selected the clips when you selected the matte in the comp viewer. To reset the scale, select them all in the timeline. Then hit S to reveal the Scale property. with all clips still selected, simply type in 100 and they will all pop back to full size. After that, you may wish to lock them using the small lock symbol to prevent further mishap. In the future you may wish to create your strobing in AE itself. There's a Strobe Light effect in the Stylize category which, applied to an adjustment layer, could operate on your entire timeline if you want to or on the respective clips, if applied directly to them.