@blackvenomm666 The second On :Connect: Cannot be working because you didn't close the first one. My guess is - You are getting a ON unknown command error and then the script continues joining the second set of channels.
You have 2 opening brackets in this event.

On *:Connect:{ if ($server == server name here ) { 

You need 2 closing brackets at the end of THIS event if you want mIRC to track the second event.
You have the correct number of brackets but they are in the wrong places.
In addition to this, you cannot have 2 On *:Connect: events in the same remote.
Also, using $server is a bad idea. It's better to use $network.
The code should read like this

On *:Start:{ .server server ip and port here }
On *:Connect:{
  if ($network == 1st network name here) { 
    .timer 1 1   .join # 
    .timer 1 5   .join #
    .timer 1 10  .join # 
    .timer 1 15  .join # 
    .timer 1 20  .join #
  }
  if ($network == 2nd network name here) { 
    .timer 1 1   .join #
    .timer 1 5   .join #
  }
}