Yeah, I seem to recall having similar trouble with a base I designed somewhere.
I think all the repulsor beams were trying to shoot at the same target. Now that I think about it, it is probably because the targeting preferences say to target ships until they are 100% damaged. If you were to set that lower (say 10 or 20%) then maybe the base would split its fire more equally.
Of course, then it might not destroy things properly
Still, you can't have everything right?