i had the same problem couple times. and i still do not know why that happends. just use an maplist from other server. or use a clean one from old server files A2 and add urself the new maps
removing the empty line from maplist doesnt work. i tryed it docent times and did not work i cudnt find the problem either i just used a diffrent maplist from A2 server files and that worked. for me and i added all maps manualy
actually, i will have to agree with conquer93, had this issue once as well and it turned out to be an issue with one of the fantasy maps, just remove the lines one by one from the bottom up until it loads, then you will find the bad line, then you can try and fix it