If you have v2.0 of the Eggbot Control extension, then yes centering was funky. If you used a 1000 px high document, then the document's centerline (y=500) corresponded with where the v2.0 EC extension assumed the pen was centered. The extension always assumed that "start with pen centered" meant that the pen was resting along the line y=500. If your document had a height of, say, 800 px, then that line of y=500 was not the centerline of your drawing.... Basically, 2.0 and earlier assumed that your document had a height of 1000 px.

With v2.1 and later of the extension, you get centering like you would expect. The Eggbot Control extension looks at your document's dimensions and then assumes that the pen is at the (x,y) point (w/2, h/2) where w is the width (3200 px) and h is the height, whatever that might be.

Dan