Add rules to url manager in bootstrap

Currently I add some url rules in my module Bootstrap class, the urls are added successfully and they work if I type them in the browser address bar. However they do not get generated (eg. in my main menu).

I found out if I add these url rules in the main config, they are being used in the main menu.

Why is this and how can I resolve this?

Anyone an idea why this is and how I can resolve this?