Hi,
It sounds like you're using Composer.
Typically an exported .mid file is truncated to the measure with the last note in it (as you've found) to avoid "dead space" at the end of a file that you've been working on.
You can trick Composer, though, into keeping those last empty measures in the exported .mid file. In the last beat of the last measure you want to keep in the file, add a single note, then hold the "L" key on your keyboard (for "loudness") and press the Down arrow key. You'll see in the status bar that the loudness for that note will go down. Hold the down arrow key til the loudness goes to 0, then press the Up arrow key once to give it a loudness of "1". This puts a viable note in the measure so that the measure won't get truncated, but the loudness (velocity) of that note is so low that it won't be heard unless you've got the volume on your speakers turned up really high.
Enjoy
Sherry