I suspect that you may also find that the size of the PPT is larger in PPT 2007 as well. When Microsoft rolled out Office 2007, they made a radical change to the way that 2007 handles graphics. I don't have all the details, however it appears that the 2003 version would compress and re-size the graphics automatically to match the finished size on your slides. The 2007 version appears to retain the original size in the PPT file, even though it will display the smaller size that you set on screen. Those full-size graphics can make PPT 2007 files explode in size. I have examples of PPT 2007 presentations that were 100MB in size that shrunk to less than 10MB when re-saved in 2003 format. (I find that PNG formatted images may cause less of this bloating than similarly sized JPEGs and TIFs.)
The differences in the way 2007 handles graphics may be affecting the file sizes you're getting from Presenter as well.