Have a look at [URL="http://www.romhackersonline.com/forum/showthread.php?t=2486"]this thread.[/URL] -- I don't have the program anymore, but this is the general process I've always used and it works pretty well for me.
The program simply filter's out any non-gba compatible colors. GBA colors are in 15bit encoding. Like so:
blank || blue blue blue blue blue || green green green green green || red red red red red
( 2 bytes; the Hi-bit is a dummy bit and has no significance. )
So, your RGB channels have a maximum value of 2[sup]5[/sup] - 1 (= 31 ). To convert this to the "standard" RGB channel, multiply the value by 8, to get a maximum of 248. This means that only every other 8 channel levels are accessible by the GBA.(0, 8, 16, 24, and so forth ). So what you should do is, after importing your palette and tileset image, find any non-working colors in advance-map, and find the [ working ] color that matches the desired color closest and replace the non-working color with that color. I know that wording is probably confusing, but that's the simplest way for me to explain it, I think.