The latest and greatest version of pacman has quite a few little changes. See the ChangeLog for details.
Notably, an %o parameter has been added to the XferCommand directive, which lets you use the -O option of wget to write to filename.part, allowing proper file resumes.
XferCommand = /usr/bin/wget --passive-ftp -c -O %o %u
Or if you want wget to shut up a bit, add
XferCommand = /usr/bin/wget --passive-ftp -c -nv -O %o %u