[CaHbKo]

pawn Code:

if(id == INVALID_PLAYER_ID)

Code only proceeds if id does NOT contain a valid player. So you don't let the script work with real players.

You do not set the id's faction. PVar[id][pFactionL] = PVar [playerid][pFactionL]?

This code

pawn Code:

if     ( PVar[ playerid][pFactionL ] == 1 ) SendClientMessage( id,-1,"Jūs priimtas į policijos departamentą" ); SetPlayerSkin( id, 120 ); PVar[ id ][ pUniform ] = 120; PVar[ id ][ pUniformc ] = true;
                if( PVar[ playerid][pFactionL ] == 2 ) SendClientMessage( id,-1,"Jūs priimtas į medicinos departamentą" ); SetPlayerSkin( id, 71 ); PVar[ id ][ pUniform ] = 71; PVar[ id ][ pUniformc ] = true;
                if( PVar[ playerid][pFactionL ] == 3 ) SendClientMessage( id,-1,"Jūs priimtas į mechanikų departamentą" ); SetPlayerSkin( id, 50 ); PVar[ id ][ pUniform ] = 50; PVar[ id ][ pUniformc ] = true;
                if( PVar [playerid][pFactionL ] == 4 ) SendClientMessage( id,-1,"Jūs priimtas į taksi departamentą" );   SetPlayerSkin( id, 223); PVar[ id ][ pUniform ] = 223; PVar[ id ][ pUniformc ] = true;

Can be translated as

pawn Code:

if( PVar[ playerid][pFactionL ] == 1 ) SendClientMessage( id,-1,"Jūs priimtas į policijos departamentą" );
                SetPlayerSkin( id, 120 );
                PVar[ id ][ pUniform ] = 120;
                PVar[ id ][ pUniformc ] = true;
                if( PVar[ playerid][pFactionL ] == 2 ) SendClientMessage( id,-1,"Jūs priimtas į medicinos departamentą" );
                SetPlayerSkin( id, 71 );
                PVar[ id ][ pUniform ] = 71;
                PVar[ id ][ pUniformc ] = true;
                if( PVar[ playerid][pFactionL ] == 3 ) SendClientMessage( id,-1,"Jūs priimtas į mechanikų departamentą" );
                SetPlayerSkin( id, 50 );
                PVar[ id ][ pUniform ] = 50;
                PVar[ id ][ pUniformc ] = true;
                if( PVar [playerid][pFactionL ] == 4 ) SendClientMessage( id,-1,"Jūs priimtas į taksi departamentą" );
                SetPlayerSkin( id, 223); 
                PVar[ id ][ pUniform ] = 223; 
                PVar[ id ][ pUniformc ] = true;

So as you can see, SetPlayerSkin and PVar operations get ran INDEPENDENTLY from pFactionL value. Only SendClientMessage depends on it.

Here's your code (note that I used commas instead of semicolons in the 'if(PVar[playerid][pFactionL] == x)' checks)

pawn Code:

CMD:priimti(playerid, params[])
{   
    new id;
    if(sscanf( params, "u", id )) return SendClientMessage(playerid, COLOR_RED,"Komanda: /priimti [ћaidejo nick / id]");

    if(PVar[playerid][pFactionL] > 0)
    {
        if(id != INVALID_PLAYER_ID)
        {
            if(PVar[id][pFaction] == 0)
            {
                new string[128],name[MAX_PLAYER_NAME]; 
                //string[128] because SendClientMessage can only send maximum 128 chars!
                GetPlayerName(playerid, name, sizeof(name));
                format(string, sizeof(string), "Pakvietei %s dirbti i savo frakcija",name);
                SendClientMessage(playerid, -1,string);

                if(PVar[playerid][pFactionL] == 1 ) SendClientMessage( id,-1,"Jus priimtas i policijos departamenta" ), SetPlayerSkin( id, 120 ), PVar[ id ][ pUniform ] = 120, PVar[ id ][ pUniformc ] = true;
                if(PVar[playerid][pFactionL] == 2 ) SendClientMessage( id,-1,"Jus priimtas i medicinos departamenta" ), SetPlayerSkin( id, 71 ), PVar[ id ][ pUniform ] = 71, PVar[ id ][ pUniformc ] = true;
                if(PVar[playerid][pFactionL] == 3 ) SendClientMessage( id,-1,"Jus priimtas i mechaniku departamenta" ), SetPlayerSkin( id, 50 ), PVar[ id ][ pUniform ] = 50, PVar[ id ][ pUniformc ] = true;
                if(PVar[playerid][pFactionL] == 4 ) SendClientMessage( id,-1,"Jus priimtas i taksi departamenta" ),   SetPlayerSkin( id, 223), PVar[ id ][ pUniform ] = 223, PVar[ id ][ pUniformc ] = true;
                
                PVar[id][pFactionL] = PVar[playerid][pFactionL];

                return 1;
            }
            else
            {
                GameTextForPlayer(playerid,"~r~Zaidejas turi darba.",5000,3);
            }
        }
        else
        {
            GameTextForPlayer(playerid,"~r~Player is not connected.",5000,3);
        }
    }
    else
    {
        GameTextForPlayer(playerid,"~r~Tu ne direktorius.",5000,3);
    }
    return 1;
}