I was not refering to the star/planet count, I was referring to the slider for map size. I made a 5 star 25 planet, and experimented with the slider to put some space between the stars...
I have played on many different sizes of maps - it is / was not that.
I had never had this problem before on 1.03 (Did not even play the game pre 1.03).
The problem, upon further investigation, I have found it could have been several factors coming into play. I posted the same question on another forum, and they said it could be heat related (Though, while having built this comp myself, and monitor my temps carefully, I know its not heat). This however, gave me another idea. After looking into it, I noticed my processor was jumping between 2.4Ghz and 1.5Ghz (And stayed on 1.5Ghz or so while not under load, and 2.4Ghz when under load) - This, as I suspected, was due to energy saving settings activated in the BIOS (Specifically, C1E and EIST), upon disabling these, the processor ran at a constant x9 muliplier and 2.4Ghz clock speed (What it should be).
This did not fully fix the problem (But did help), after trying a new game (I was getting lazy and using a save game), the problem was minimal but still there (The BIOS settings reduced it quite a bit). I then tried reverting my mod back to the one I gave a friend of mine. I did and still do not see how modifying the max hull points - which is the only thing I added after I gave it to him - caused the stutterin, but it seems to be mostly gone.
I can't say its 100% gone, but I have not noticed it (I have not played a full game though, yet. Have not had a chance).
Thanks for your replies, I will update this post if it is / has gone away for sure (And if it has not ill continue trying to find the cause of it, and update it - maybe it will help some one else find the cause of their stuttering).