A cap is purely there to provide you with power when you have a drain on normal load, I.E a heavy bass section and I would imagine that continual driving of a sub will not allow the cap to get back up to its full storage capacity so in theory your draining it before its been allowed to fill back up.
Like trying to fill a bath with the plug out.
Maybe try one of a higher farad rating as it sounds like the one you have isnt up to the job.
