I haven't been able to reproduce the problem. I'm running on a Mac but that shouldn't make a difference.
One thing to note: it is actually the suffix of the file name that you select for the output image that tells IGV which type of image to create. When you select to save an SVG file, the default file name will have the .svg suffix, and when you select to save a PNG file, the default file name will have the .png suffix. You can see the destination format from the file name suffix in the window that pops up before you click save. In fact at that point, you can change the suffix to control the image type created. Please let us know if the file name suffix is .svg when you click save and it still creates a .png file.
-HT