Most likely because of Peukert factor. I've had a Link 2000 in for 15 years and never bothered with the small discrepancy, because it's not a discrepancy but rather a reality of
battery performance.
AH out is a measure. The
depth of discharge, i.e. 5A vs. 30A affects the remaining capacity. Higher the load eats more % of total for whatever time it is on.
At least that's my layman's language understanding of it.
Once you've lived with it and on board and regularly checking the numbers, and end up becoming intimately familiar with what you think they should be and confirm it only then by looking, it will become even less of an issue.
I even guess and write down what I think it will be when I arise the next morning.
Just talkin' operationally and management-wise, not evaluating the engineering.
Interestingly enough, just last week I made up a blank spreadsheet and wrote down time, V, A (instantaneous), AH, and what's on or not (fridge, phones,
VHF, etc.). I didn't
record the % 'cuz I never have used it since I zero in on V and AH. I do this periodically to check up on the condition of my house bank. I have 200 ah out of my 400 ah bank.
Good luck, I can't wait to hear the REAL reason!

Great question, thanks.