Khaled: I first noticed the issue on 7.1, was able to replicate it on 7.12beta (just downloaded today) in an empty install folder (portable install if it makes a difference, OS is XP).
I just did the same test as you (on EFnet, was using DALnet before):
Session Start: Mon Oct 11 17:51:32 2010
Session Ident: testotron
01[17:51] <testotron> this is the first line
[17:51] <testotron> this is the first line
01[17:51] <testotron> this is the last line
And in a channel:
Session Start: Mon Oct 11 17:52:48 2010
Session Ident: #randomchan
03[17:52] * Now talking in #randomchan
03[17:52] * irc.he.net sets mode: +nt
Where as there is "<@testotron> this is the last line.." as the last line in the chan window.
I'm using "tail" in this case, however also checked just opening the logs with notepad.exe with the same result.