Ah, I was incorrect. Your problem is likely you are using paths for the pads. Fritzing uses the circle diameter and stroke-width in a python script to generate the gerber output, while I've seen a number of people (even in core parts!) use paths for pads, I've never seen a case that worked correctly. Here is the connector xml from a generic 16 pin connector from core (what I had easily to hand ):
<circle cy="70" gorn="0.2.0.0" stroke="rgb(255, 191, 0)" fill="none" r="29" stroke-width="20" cx="70" id="connector0pin"/>
<circle cy="170" gorn="0.2.0.1" stroke="rgb(255, 191, 0)" fill="none" r="29" stroke-width="20" cx="70" id="connector1pin"/>
if you substitute this in to your svg it should work better. This sets the hole size to .038. If you need something different (and are using Inkscape ) it is set by circle diameter (in inches) - stroke-width * 2. In this instance the diameter is .078 - 40 = 38 thou (note sometimes Inkscape uses odd units in stroke width and this then doesn't work right) which gives 38 thou as the stroke width is 20 (and units this time in xml editor are in thou). You are usually best to start from either a generic IC from core or a generic connector from core both of which have appropriate settings in the svg. The trick to the svg image (as I have just discovered lately) is to right click on it and then save as image to recreate the svg. Sometimes the forum won't render the svg and then I don't thing that works, but in this case it did.