While I haven't used this tactic myself in an actual game, I have experimented quite a bit with the placement. At first, I wasn't sure it was possible-so I had to test it.
Due to partial tiles counting as within the area of a starbase, you can have up to 24 starbases affecting a total of 2 (that's right, TWO) tiles.
I've used hyphens so the spacing will hold; hopefully it's clear enough.
It goes a little like this:
The x's are your starbases. The line in the middle is just the sector line; don't worry about it. The eight in the middle two sectors can be placed in alternative positions, as far away as the lowest/highest outside ones (maybe one more tile than that) and still affect the same specific tiles. The O's are the two tiles in question which receive the full bonus from all 24 starbases. They are eight parsecs away from either neighboring sector-right smack in the middle.
If memory serves, they max out at +54 attack and +9 defense. Times 24 is +1296 attack and +216 defense.
My guess would be you simply don't have them underneath the array for long enough, though I'm not sure how long "long enough" would be. Hopefully someone else can help you in that regard, but I do have a couple of additional points that may be helpful. Also, I would recommend using a large or greater galaxy size, along with at least common/common planets/habitable as a general rule, just so you can build fast enough.
As a note, defense influences your military score as well-though only on ships with at least 1 attack. Formula should be total attack of all ships + total defense of all ships + (total hp of all ships/10). Try building a ship with only one weapon and fill the rest of it up with EOL defenses-zero point works nicely. Watch what happens.
Mostly useless for an actual game, due to the way combat is handled in DA, but it does actually count as more for your military score than a comparable ship with all weapons. I'm not positive this holds true for all weapon/defense possibilities, assuming same tech generation, but it holds true for a significant portion of it, including the final techs...which should really be all that matters. Additionally, maxing out a defense tree takes between 12k-17k research (base cost, before tech speed is factored in), while the cheapest weapons tree takes ~49000 to max out (beam weapons), and isn't a particularly good size/space ratio.
This is particularly effective with the Krynn, who start with a +50 defense bonus. Starship Defenses adds another 10% on top of that, and Universalists adds another 10% for practically free. The luck bonus doesn't hurt, either-if you spend one customization point, you're at 50% luck, and always have your weapons roll from half to max. Even without the Krynn's +50 defense bonus, the +20 from starship defenses and universalists is more than enough to overcome the 25% boost to attack that ships in orbit get, due to the extra amount of defense one can place on a ship as compared to weapons. In addition, you can only have 10 ships in orbit per planet, so that 25% is limited.