Potential only affects how much you can train a player before you get reduced rates. It doesn't affect salary or training speed or anything else. Differences in salaries are usually due to sub levels, or fraction of levels that you can't see on a player's page but that affect his play and his salary.
Also the salary calculators are a little out of date which can cause some small discrepancies as minor adjustments are made to the formula at the end of every season.