If your torrents are getting and/or staying paused despite your efforts to restart them, here are some things to try:

It often helps to chose ruTorrent's 'General' tab & select the paused torrent for various information.
 

Some reasons torrents might be pausing automatically:

1. Full disk. You can check the free space in ruTorrent by clicking on a torrent and scrolling down in the 'general' tab where is will say 'Disk Free'.
2. Momentary and random write errors.
3. Removed or incorrectly moved data, other errors.

Some steps to take:

1. Clear up disk space if needed. - rtorrent will auto-pause torrents when there's not enough free space to download them.
2. Stop, & then force re-check the paused torrents, then try restarting them again.
3. Confirm the data is there &  in the right place.
4. If none of this works, try rebooting your seedbox through your Dashboard. - Remember to give it approximately 5 minutes to come up again, and then try stopping/force re-checking & starting them again.