I uploaded a new version of the map compressor last night which produces smaller filesizes (if the images are in your DF folder, so it can find your init file and font bmp), and can better handle images which have abnormally high levels of color variance (e.g. your white statues do not look like what they mathematically SHOULD look like, and there may be more than one white statue image in the exported map images, which are not pixel-by-pixel identical, but are similar). The color match threshold is user-modifiable, and the compressor will detect a moderately high unique tiles ratio and ask if you want the color match threshold turned up to compensate in case it's this kind of an issue.
I've also included more detailed instructions on running it with MONO for people who aren't on Windows. For those of you on Ubuntu, I would suggest getting it directly from the Mono website - they have a .bin installer - so you KNOW you're getting what they wanted to release for 1.2.6. If you just try to get Mono from your package distribution thingy you wind up with 1.2.4, but won't be able to run the map compressor at all. There are possibly devel-tagged versions in the ubuntu package dist system but who knows if they are the beta or the final versions, and they're tagged with warnings that they MAY NOT WORK ON UBUNTU BLAH BLAH ETC. I'd say just get it from the Mono website.
P.S. The filesize improvements did not require a change to the fdf-map format, only an improvement to the program itself - specifically, it is able to identify the random ,.`'% tiles in the blackness, and change them into black tiles, and so compress those all more effectively. Since that doesn't require a change to the file format, it doesn't require a change to the map viewer either. There is another filesize improvement which I coded, but it is disabled until Markavian has time to update the viewer to support it, at which point I'll release another version with it enabled.