I didn't do much research into this, but I found it serious and frequent enough to report.
Many downloads I tried resuming ("stop" action and later "start") cleared the partial download.
System: Ubuntu (snapshot of soon-to-be-7.10)
Options: 2 max jobs, 1 thread per job, download_folder=/home/etrusco/temp_download
PS. I just realized that although the hint in the toolbar says "Stop" the menu item says "Pause".