The generated map apparently uses the randomizer seed as the file name, but it's in scientific notation, so only the first 5 digits reliably match the seed the player enters. If two maps are made using similar seeds where the difference falls in the last 3 digits, the second map will overwrite the first.

My most recent game universe is 5.55556e+007.sts with a seed code of 55555555, I tested to see if this might be a problem by creating a new map with seed code 55555602, which was a different size (so it was definitely a different map), but it overwrote the first map because the file name was still 5.55556e+007.sts

Are you storing the randomizer seed in a float? An unsigned int might work better.