If you take a look at the address book you can see that the color of your nick is applied to "me" instead of the real nick.
After using a workaround (I had put manually "$me" in the address book with the right color and it worked well), I have found where is the problem.
Here is the little patch:
file ialias2.mrc
lines 358 and 359
/!\ Be carefull, I have applied the fix pack found on irc (#invision@irchighway)
-----------8<-----------------
while (%ct <= $scon(0)) {
.cnick $iif(($scon(%ct).me != $null && $scon(%ct).me != YourNick),$scon(%ct).me,me) $r.glob(Nick.Colors,Color.4)
-----------8<-----------------
The only modification I made is the replacement of $scid() by $scon().
$scid() uses a parameter which is a connection ID and $scid(0) returns the number of active connections.
$scon() does the same thing but uses an integer rather than an ID so it's better to use it in loops.
The problem here is that connection IDs are incremental.
So, you can have for example 4 connections but there IDs can be greater than 4 (for example: 5, 21, 23, 86).
With theses numbers, the loop used is wrong because it tries to access the connections this way:
-> ID = 1 => $null
-> ID = 2 => $null
-> ID = 3 => $null
-> ID = 4 => $null
-> end of loop because there is only 4 connections
By using $scon() the loop is correct:
-> $scon(1) => $scid(5) => OK
-> $scon(2) => $scid(21) => OK
-> $scon(3) => $scid(23) => OK
-> $scon(4) => $scid(86) => OK
-> end of loop
And here, we don't drop any connection in the loop.
End of the (long) explanation of the problem

Thanks Cryoa for this great script and also cnils and krypton for their efforts solving problems and releasing fixes.