Well, that could be the case. In my experience with image manipulation so far, the pixel-to-pixel should be the same. That's why I asked how he was getting the pixel count from the GIMP. If he was measuring by anything other than pixels in the GIMP, that would explain the problem (unless the image was set to 100% zoom and he absolutely knew the pixel resolution per unit of measurement.)
I use PaintShopPro, not the GIMP, so I couldn't say for certain how to change the rulers in the program to pixels, picas, or anything else, for that matter. Generally, what I have been doing is importing individual renders into a Microsoft Publisher document I've set up with a grid of guides set to certain pixel lengths, crop as necessary, expand to individual cells, and export as a PNG at maximum resolution. Then I bring it up in PaintShop, mask it, and resize it to the appropriate size and I make sure that I do that in pixels, not in any other unit of measurement. So far, that's worked out well for me. I think the last step is the crucial one.
Here's where I'm fuzzy: if the ship is importing into EVNEW at the size you are specifying it at, you need to know already the pixel count of the whole image and the individual sprites. So, you already know how big the image is in pixels. You should be able to get a clear pixel radius from that, and at least be able to guesstimate within close reason where your weapon exit points should be.
Hope that clears anything up!