Which flotilla cfg are you looking at ?
data\Cfg contains the flotilla cfg that will allow you to start from those bases
The start co ordinates need to be the same as the LND entries for those ports
The data\menu\Cfg\Menu flotilla cfg controls where the base is placed when looking at the start map and is a bitch to get correct
Trust me have spent many an hour on it - note position of 30th\33rd flotilla