Just to confirm what you are talking about:
On your local development machine you are running as a server and using php - this does not work. You get the black background
When run with the shell on the same machine it is OK and you get the transparent background.
You have not tried it on the online server which is running 6.0.7
I presume the problem must be something to do with the way the code is being interperated?
This works for me using XAMPP on windows XP:
exec("convert 2007_1226christmas0004.JPG -format PNG32 -background transparent -thumbnail x330 -resize \\"440x<\\" -resize 50% -gravity center -crop 220x165+0+0 -rotate -4.4 output1.png 2>&1", $array);
Note if I use -resize \"440x<\" it works but if I use -resize '440x<' it fails. This is just something to do with windows.
Version: ImageMagick 6.3.7 11/14/07 Q16
I can use either on my server and they work Version: ImageMagick 6.3.5 08/29/07 Q16
I have had nothing to do with OS X and presume it must be something similar with the way the code is written ?
P.S. If I use the XP command line I must use -resize "440x<" not -resize '440x<' as well.