This has been an interesting thread, I'll have to take this into account while designing my missile catcher ships!
I did the same and the design faild. I suspect a bug in low-to-hit cases.
I setup some scenarios to replicate your bug in the bug thread, and I think I figure out what went wrong.
In short, if the final hit chance is between 0.5% and 1%, the display will round it to 1, but the actual hit chance will be rounded down to 0. If the final hit chance is slightly higher than 1%, it seem to be working as expected.
My setup: incoming missiles at 100kkm/s, turret tracking speed 40kkm/s, missiles have ECM 6, BFC has ECCM 2, BFC 10kkm accuracy 98%, 10% size gauss
Test 1: Active range against 6MSP is 14,419,238 km, the missiles can traverse this distance in less than 29 ticks, so the final tracking bonus is 28%. In this case, hit chance can be calculated as:
( (40000*1.28/100000)*0.98 - (0.6-0.2) ) * 0.1 * 100% = ( 0.50176 - 0.4 ) * 10% = 1.0176%
The displayed interception chance is 1%. The interception used 16650 shots out of 18000 available shots to intercept 180 incoming missiles, which gives an accuracy of 1.081%
Test 2: Active range against 6MSP is 13,894,726 km, the missiles will spend less than 28 ticks in this range, so the final tracking bonus is 27%. In this case, hit chance can be calculated as:
( (40000*1.27/100000)*0.98 - (0.6-0.2) ) * 0.1 * 100% = ( 0.49784 - 0.4 ) * 10% = 0.9784%
The displayed interception chance is still 1%, however the interception hits 0 out of 18000 available shots.