If you have special rates XML-enabled on booking.com, that allows us to manage the percentages for those special rates. When enabled, you are able to set a percentage discount for those rates directly in Myallocator, as shown below:
As you see in the screenshot above, there has been a 5% discount applied to the Non Refundable Rate.
However, when looking in your booking.com extranet page, you might see something like this:
Non-Refundable Rate - 7%
The 7% does not match the 5% rate specified in Myallocator.
If this problem applies to you, please contact booking.com directly. Those special rates may be connected to the standard rate in a parent/child way, and if so, changes by the channel manager are not allowed. Booking.com will need to eliminate the parent/child relationship, so that the percentages set by the channel manager will be considered.