Use the ImageMagick convert with the "-flatten" option for the background. The actual "PDF" thumbnail conversion is passed to GhostScript as a delegate which means both must be installed on the server correctly. If done correctly which happens in most cases, the path for GhostScript within your coding is not needed if using ImageMagick. The actual PDF encoding can also be a problem. There are shared hosting accounts running 7 year old versions of both ImageMagick and GhostScript with no problem on PDF conversion to thumbnail within the current stable TYPO3 CMS 6.1.1.
A free direct download PDF test file with detailed instructions to solve a "PDF Thumbnail Generation Problem" in TYPO3 CMS is available at Smargasy, Inc. "http://www.smargasy.com/fileadmin/media_data/community/Smargasy_PDF-Thumbnail-Compatibility-Test-File.pdf". The test file helps isolate the problem on systems that use ImageMagick and GhostScript as the image processing and conversion program in a shared hosting environment.
Best Regards