How to convert variable frame rate videos?
Have you tried using Quicktime Pro version 7?  It's what I usually use for file conversions.  It costs about £20 / $30.

http://store.apple.com/uk/product/D3380Z/A/quicktime-7-pro-for-mac-os-x

Open your file.  

Go to the file menu, and select Export
Choose your format, e.g. Quicktime Movie with ProRes 422 codec at 30 fps.