It does matter what format the footage is - avi or mpeg4 - that doesn't affect the size of the video. Perhaps one file is 1080 and another is 720, or one is HD and one is SD, that is likely the issue.
You can right-click each clip in your bin and see the properties that ought to tell you frame size and frame rate, etc.
From there, decide which size you want to work at and use that for the Sequence setting. In Preferences, there is a checkbox for "Scale to Frame Size" and this will automatically scale clips to fit, upon import (does not affect clips alreaady imported, but you can right-click those clips in timeline and manually check "scale to frame").
A tip - generally, decide how you will deliver the video, and that will help determine what size to edit at. If you are mixing SD and HD clips, but do not intend to deliver the final edit as HD - it will be DVD - then edit in an NTSC project (SD) and downscale the HD clips. If you upscale the SD clips to HD in the HD project, then they have to again be downscaled for DVD and you've destroyed the quality of the SD clips with the up/down scaling processes!
Hope this makes sense
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