AVI (probably MP4) cannot be output correctly

I have this video source file which plays back fine in Windows Media Player or VLC, but does not playback well in Premiere.  If I try to step through frame by frame it will repeat certain sections over and over and act strangely.
I really want to get a usable file that I can edit and manipulate so I've tried to load into Premiere and just output it to a noncompressed format as well as some minimally compressed formats.
No matter what I do, the output file ends up with strange freeze frame and skipped frame issues and is not an accurate copy of the original.  The source file is an AVI and VLC says it uses the MPEG-4 codec.
Can anyone tell me if there is a way to get this file (which as I said plays back fine in WMP) to be converted accurately into a format that can be manipulated in Premiere (or After Effects)?

To answer your question -- I'm using 25fps Desktop video at 704x480 for my sequence settings.
I can't replace the footage with better material because it's from a surveillance camera.... which are notorious for producing crappy and highly compressed video.
What happens when I step through frames in Premiere or After Effects is that it will step through a few frames, then as I step forward again, it will jump back in time and then as I continue stepping  I'll see the same sets of frames again and again.  It's like it's repeating entire sets of frames -- instead of just duplicating frames (like it might if the original material was at a lower frame rate).
Since the video plays through somewhat choppily (but correctly) in WMP,  maybe the footage should really  be running at 8 or 10 fps instead of the 25 fps output file that I received. And rather than seeing duplicated frames in Premiere when I move frame by frame -- I'm seeing repeated 'sets' of frames -- maybe due to very infrequent temporal keyframes or just plain bad encoding? (Has anyone else ever seen this?)
When I try to re-encode it I get lots of freeze frames -- and I'm starting to think that's what the video is supposed to look like.  When I'm stepping frame by frame in Premiere (with the original material), I'm starting to think it's not an accurate representation of the file.. but as I said, instead of duplicating one frame 2 or 3 times, it's duplicating groups of frames. 
It's just such a strange file and I've never seen Premiere act so unpredictably before -- but I'm definitely starting to feel that the re-encoded files I've attempted are actually correct and it's only the frame-by-frame viewing that is wrong, instead of the other way around. 
Thanks for everyone's  input -- if anyone has other ideas, I'm open to hear them, but I think the problem might be solved.

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