Cropping with media encoder withour black lines

I found a number of similar posts, but none solve the same problem I have:
When I save a video in Premiere CS3 with the media encoder, I get black lines on the sides of the video. I noticed that I use crop (in the encoder) of 4:3 but it actually gives me a window that isn't of that exact size (for instance 200X151 pixels). I save the video (in MPEG-2) in size 360X270, so the extra pixels might be the cause of the black lines.
When I crop to some rectangle and save the video in the exact same pixel sizes (not just ratio), I don't get the lines.
Anyone have any ideas on how to get rid of the black lines?
Thanks!
Aya

The project settings are desktop editing, 30 fps, size 360X270, square pixels, lower field first (I don't know which settings are important for this)
The video I load is with codec VP6F (FFMPEG) - I have flv and using virtualDub I converted them to avi, trying to keep the original quality (which isn't too good to begin with), so I could work with premiere.
Then, in premiere, the only way I found to crop the video (without it being resized) to the size I wanted was to use the media encoder, and only MPEG-2 codec (for some reason all other codecs that I tried resulted in a movie with problems, like jumping or blurring)
I've been working for days trying to get an flv into premiere, then cropped and edited in premiere (I cut short clips from the original movie) and back to an avi with some standard codec.
The main problem is currently the black bars (but any general suggestions would also be helpful :). The only way I managed to somehow get rid of them is to save the movie in the exact size of the cropping (which isn't really good, because I need to resize). But then when I open the video in VirtualDubMod it has black bars again...
Help!
Thanks,
Aya

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