It has nothing to do with Ludicrous map size. It does this on ALL map sizes.
And yes, there is a way to fix it. I alrdy figured out how entirely on my own (since, as is often the case with the endless problems in these games, there were no answers posted online), and fixed it in my mod last February.
You have to change the XML, either with a mod or by editing the base game file directly. In "GalCiv3MapDefs.xml", fairly near the bottom, change the values on these two lines to read this:
And presto, player home systems are now pretty close to evenly spaced, which is mandatory for making the game playable in my opinion. I think I know the reasoning/rationale behind why they did it the way they did instead, but I vehemently disagree with it.
Normally I like to keep stuff like this that I've figured out on my own private, but in this case it's SO egregious a problem that I felt compelled to share so at least a few other people wouldn't suffer. You're welcome.