This should fix the issue if the problem is what I think it is. If you open up line 523 of threads_import.php. The code looks like this:

Code
$groups = split("-",$user_data['U_Groups']);

// Insert into USER_GROUPS
foreach($groups as $k => $v) {        
     if (!$v) continue;

Change that, to this:

Code
$groups = split("-",$user_data['U_Groups']);
$done = array();

// Insert into USER_GROUPS
foreach($groups as $k => $v) {        
if (isset($done[$v])) continue;
   $done[$v] = 1;
   if (!$v) continue;