There may be genuine variations in the stroke thicknesses, depending on your drawing program and how you're keeping consistent stroke thicknesses. Also, since it isn't a font yet, it is unhinted, so you've got the random factor of how it will round to the rasterization grid of the output device (printer).

To do small size samples, you'll want to move it into a real font editing program, and have it hinted. Of course, these days there are only a few of us who will recommend Fontographer. If you're on a budget, consider TypeTool. Otherwise, look at FontLab or perhaps DTL FontMaster if you're doing full-time font production.

Regards,

T