Other than used from Port Royale 2 it is not sufficient to bump other ships in boarding mode to board them. Instead, you have to sail sail a certain time abreast until the boarding circle is totally filled green. Normally the opposing ship is highly damaged at this stage of sea battle and therefor slow. Is you own ship in good shape, you will pass your opponent too quick for successful boarding.
You have to lower the speed of your ship by pressing and holding the button “Q” on your keyboard. This will shorten your sails and you will become slower.
This hint is unfortunately not to be found in the manual.