DEVONagent Pro uses OS X's Services internally to transfer data to DEVONthink. If DEVONagent Pro beeps when you try to transfer data to DEVONthink, the most likely reason for this problem is that there's something wrong with the Services.

You can use the third party application Service Scrubber to try and modify this behavior; Service Scrubber should allow you to enable/disable services, rename them, or give them new keyboard shortcuts. Some of these modifications, however, can lead to communication problems between DEVONthink and DEVONagent Pro. Restore to the default settings to enable the DEVONagent Pro/DEVONthink link again.