The commission is saved properly but has wrong value

If you are able to track the sale/lead commission, but it has a wrong value, there can be few problems.

check your commission settings - "fixed cost" means the value is subtracted from the original total cost, and then the commission is computed (so the final commission is different than the expected one)
"Top Level Affiliate Commission" plugin activated (or any other plugin) can cause this confusion too... it gives % commission to top level affiliate
check your sale tracking code - there is an option to hardcode the commission, so maybe this is your case