It may be you need to change some exporting options. My memory's fuzzy on how I named things (I wrote the JT .x exporter), but there's one that interpolates matrix keys between your key frames that you can turn off (if it's on--I think by default its not). It was there for systems that don't interpolate key frames. Instead of matrices you should be able to use the translations and rotations which also are options. Or could you just be confused about the gaps in the key frame numbers in the file? I used the DXSDK tiny.x sample as my convention for timing, which assumes a much higher resolution on timing.
-John
John Thompson
http://www.jtgame.com/jtedit