Glad you found it.

MessageLocaleID is set after the user selects the language which is after the login screen.

You are right

I checked the Turkish translation and apparently the key for this message is translated, as follows:

<msg_key>SFSM_UserDeactivated</msg_key>
    <msg_language>1055</msg_language>
    <msg_text>{\rtf1\ansi\ansicpg1252\deff0\deflang1033{\fonttbl{\f0\fnil\fcharset162 Tahoma;}{\f1\fnil\fcharset0 Tahoma;}}
\viewkind4\uc1\pard\lang1055\f0\fs18 Bu hesap \'feu anda aktif de\'f0ildir. Sistem y\'f6neticisine ba\'fevurunuz.\lang1033\f1\par
}

Are you sure that by the time the login form is presented to your user, the MessageLocaleID is set to 1055?

When the account is not active is marked in the Security Editor for a user, the user gets

"This account is not active. Please contact your administrator."

message, but this message is not localized to Turkish.

Could you please help us to localize this message?