Description:
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Imagerotate between -45 an 45 degree including an alphachannel is no problem! 46 to -44 ist still replacing the background with black.
Ohh i forgot: If you rotate, you have to specify an backgroundcolor by imagecolorallocatealpha(!) and set imagealphablending to false and imagesavealpha to true to get an transparent rotated png...

Reproduce code:
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<?PHP
$rot = 35;
$i = imagecreatetruecolor(300,300);
imagealphablending($i, FALSE);
imagesavealpha($i,TRUE);
$whitetrans = imagecolorexactalpha($i,255,255,255,127);
imagefilledrectangle($i,0,0,200,200,$whitetrans);
$o = imagecreatefrompng("./rotate.png");
$o = imagerotate($o,$rot,$whitetrans,0);
imagecopyresampled($i,$o,0,0,0,0,300,300,300,300);
imagepng($i,"test".$rot.".png");
?>

Expected result:
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This works fine and copys a transparent PNG with 35 degree to the new test.png.
If you change now $rot = 35 to $rot = 46 the rotated png will appear on an black background.