Sorry to wade in here since I'm not so up on this stuff. Boy, though, Asmala can rip those formulas right off his head.
Other than the items mentioned below:
Are you fighting in a location receiving any combat adjustments by a religious facility?
If his ships have scored a lot of kills, I think each ship goes up by 1% for each kill, so that may account for a percentage difference.
Same goes for fleet but it seems fleet experience doesn't go up any more...well, at least for me...
Also, a comment on the range calculations (again, I admit to not doing proper research and that others here know these things like the back of their hand)...I thought firing from the adjacent sector had a base chance to hit of 99%.
Finally, you mentioned testing. If you did some testing in the simulator, forget it!