File error when importing .mp4 files

Hi there,
I have a problem concerning importing files.
I had some .mkv files, which I converted to .mp4 files with just 1 audio track and no subtitles using Handbrake.
Problem is, I can't import these files into Final Cut Pro 7.
It gives the following error:
"File error: 1 file(s) recognized, 0 access denied, 1 unknown."
I have no problem importing .avi files, or .mp4 files that haven't been converted.
Does anyone know what I should do? I don't know any other program to convert .mkv files, so basically, I'm bound to using Handbrake.
Thanks in advance!!

I didn't know Handbrake was such a bad tool.
I never did much video-editing before, so I usually used iMovie, and the Handbrake-converted files worked fine with that.
And I did what you said, I converted the video to .mov with MPEG Streamclip, using the mentioned presets, but now I have another problem.
A 22 minute file, which was 360MB before converting, turned into a 6.2GB file after converting.
Since I use videoclips from a TV Serie, which has over 60 episodes, this is going to cost a lot of space. Is there any way to reduce the filesize without destroying the video quality, or is there any, ANY, way to make FCP accept .mp4 files?
I don't care if it slows down my Mac or anything, it's just that I know it's possible, with the 700MB file from one of my posts above.

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