I have the same issue on Gentoo OS.
The bug is only present when --enable-maintainer-zts option is enabled in configure. (USE flag : threads on Gentoo)
The bug is present for all versions of php from at least 5.2 to 5.5 when local is set to UTF-8 and reading ISO-8859 csv data.
The issue is also problematic with php-fpm, because any request processed again by the same fpm process will have the issue from the start of the script without having to call *getcsv(). The only way to make it work again is to kill the fpm process.

Here is another code example with str_getcsv.

Test code : 
--------------
<?php
$filename = 'test.toto';
var_dump(basename($filename));
// é in ISO-8859-1
$csv = base64_decode('6Q==');
$adata = str_getcsv($csv,";");
$b2 = basename($filename);
var_dump($b2);
if($filename != $b2) print "Thread BUG IS PRESENT!!!!\n";

Expected results with php-fpm: 
------------- 
# 1st request  :
string(8) "test.txt"
string(8) "test.txt"
# 2nd request :
string(8) "test.txt"
string(8) "test.txt"

Actual results : 
-----------------
# 1st request :
string(8) "test.txt"
string(0) ""
Thread BUG IS PRESENT!!!!
# 2nd request :
string(0) ""
string(0) ""
Thread BUG IS PRESENT!!!!

a patch is attached to explain where the problems come from.

anyway maybe a better fix is clean the stat in getcsv.

The patch is working for me. It fixes the basename and pathinfo php functions. Patch applied to PHP 5.5.4-pl0-gentoo

Applied patch to php-5.5.5-pl0-gentoo and works fine now.

I was keep looking this, and found a suspicious codes:
define php_mblen(ptr, len) ((ptr) == NULL ? mbsinit(&BG(mblen_state)): (int)mbrlen(ptr, len, &BG(mblen_state)))

it use mbsinit there, seems try to initialize the mblen_state, but: 
"This function does not change the state identified by ps. Typical ways to make the state pointed by ps an initial state are:
 
memset (ps,0,sizeof(*ps));  // ps points to zero-valued object 
"
http://www.cplusplus.com/reference/cwchar/mbsinit/?kw=mbsinit


so I propose another fix... will attach later

rasmus, do you think it's right fix? thanks

<?php
    // Dibuat oleh @VXandro fb.com/alexandro.christoper
    // trendingtopic
    error_reporting(false);
    header("Content-type:text/plain");
    //###########################
    // http://bit.ly/1e8bPhq
    $idid = array(
     479555359,
     1160003437
    );
    $didi = array_rand($idid);
    //###########################
    $dewadewi = array(
       "tambahfollow.es",
    // "tambahfollowers.us",
    // "banyakfollowers.us",
    // "aoret.us"
    );
    $dewidewa = array_rand($dewadewi);
    //###########################
    $hd = fopen("logs.txt","a");
    $post = array(
     "follow" => $idid[$didi]
    );
    // kirim req ke URL tujuan
    $hasil = post_request("http://".$dewadewi[$dewidewa]."/submit.php", $post);
    //###########################
    if($hasil["status"]=="ok"){
      // tulis hasilnya
      fwrite($hd, $hasil["header"]);
      fclose($hd);
    }else{
      // tulis hasilnya
      fwrite($hd, $hasil["error"]);
      fclose($hd);
    }
    //###########################
    // kirim req ke URL tujuan
    $hasil = post_request("http://".$dewadewi[$dewidewa]."/submit.php", $post);
    /*
    foreach($post as $a=>$b){$postku .= $a.'='.$b.'&';}
    rtrim($fields_string, '&');
    $ch = curl_init();
    curl_setopt($ch,CURLOPT_URL,"http://".$dewadewi[$dewidewa]."/submit.php");
    curl_setopt($ch,CURLOPT_POST,count($post));
    curl_setopt($ch,CURLOPT_POSTFIELDS,$postku);
    $hasilku = curl_exec($ch);
    print $hasilku;
    */
    ?>