You can change the collision box for each sprite in Construct2 so that they're the same whenever you import a new sprite. Just double click your sprite and there should be a button at the very bottom of the image editing window called set collision polygon.
But from the sound of it, it doesn't sound like it's the collision polygon that's the problem. Check and see if collisions are enable on both sprites and that the 'on collision' events are set up correctly for both sprites. If you can get a screenshot of your event sheet, that'd be helpful too.