ImageMagick cannot compress PDF without loss. If you have a Linux server, you can try pdfconcat (which resets the merge very quickly):
$ wget -O pdfconcat http://www.math.bme.hu/~pts/cvsget.cgi/u=bin.i386/p=/M=bin.i386/c=f1/n=/bin.i386/pdfconcat
$ chmod +x pdfconcat
$ ./pdfconcat -o output.pdf input1.pdf input2.pdf input3.pdf
source
share