I believe servers.ini is unrelated to the use of IRC .url shortcuts or irc:// links in web pages. I just updated my servers.ini and I believe anytime I edit entries in Tools -> Options -> Connect I am editing my servers.ini. Maybe you could be more specific about why this might cause the problem I've described.
Another forum user, littlecramp, has also described the same problem in this
post. I've also send a private message to littlecramp looking for the solution.