Probably the problem is, that moodle calculates the letter grades (and all other grades, even those based on numeric scales) on the basis of percentages.
I encountered a similar problem when I wanted to show my students their final grade as a mark (swiss marking system, minimum 1, maximum 6). I generated letter grades from 1 to 6 in steps of one tenth. The final grade should be calculated as a simple mean from marks (letter grades) of tests. When I entered the shown letters/marks of the tests in the gradebook in an excel-spreadsheet, the final mark (mean) was slightly different from the one moodle calculated, but relevant for the final mark a student gets (because of mathematical rounding to steps of one half, e.g. 4.5, 5, 5.5 etc.).
I then switched to show every value in the gradebook table as a percentage and the calculations matched exactly the ones made by hand. That's what leads me to this suggestion.
Hope, this explanation and my english is clear enough and matches your question… as it is my first forum contribution here…