@r3d007so i decidedto solve the mystery of why you had to put the bios' in the roms folder. if the retroarch.cfg in /opt/retropie/configs/all/ does not have the line:
system_directory = "/home/pi/RetroPie/BIOS"
or it is #hashtagged out, or you edited the retroarch.cfg for those systems either manually or through the retroarch gui, that made major config changes then you need to put them in the roms folder. to fix this open up /opt/retropie/configs/all/retroarch.cfg and see if that system directory line is in there. if it is #hashtagged out, remove the hashtag and save.if it is not in there, then add it. if it is correct open up the retroarch.cfg in the individual systems config folders and find the issue and delete or correct it. the rgui can mess things up when you are using it, hence why i never use it to configure anything other than core-options.