I advice to use mods mentioned in the beginning of the 1st post of my recent "Epic way to play FTL" topic -
here. I did a few runs using those mods, and never encountered the problem you described as long as i "keep exploring deep space" (i.e. don't progress to further numerical sectors). There is a link there with further details and mods themselves.
Obviously, you don't have to play this "Epic" way i described, too - do however you like. Those mods are great overall for many purposes.
