Render Queue Slows Down with Large Queue

I recently bought a 2014 Mac Pro for the specific purpose of rendering large volumes of After Effects Compositions.
I am rendering approximately 40,000 After Effects Compositions - the reason being that I am using an After Effects Script to create personalised videos from a CSV file.
I've segmented the list into batches of around 1,000 at a time and each film is 1m25s long. I am also using the Mercury Playback Engine GPU Acceleration (OpenCL). The videos are added from After Effects into AME.
The Problem
When I start the render, it churns them out at about 3 minutes per video. If I leave it for more than around 9 hours, the render time dramatically slows down. After leaving it for more than 24 hours (a weekend) I've seen render times of around an hour per composition.
Question
Is there a way to stop the queue from slowing down?

I've noticed it with more than 40+ objects in the Queue as well. Now I just save the Queue and stop and exit and re-open if it looks like it's slowing down. Mind you this is a 4Ghz Hex core, 64GB Ram and Quadro 5000 + Tesla C2075 so I know it's not a system issue. CC prior to CC (2014) I never experienced this issue.

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JMS Queue slows down after time

          Hi,
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          Hi Tom, The memory usage is fine. 1Gb is available to the JVM and the memory usage
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          Tom Barnes <[email protected].bea.com>
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          >> Hi Tom, We are able to measure a slowdown by the time it takes to post
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          >> Tom Barnes <pleasereplyinnewsgroup.weblogic.developer.interest.jms@newsgrou
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          >> ps.bea.com> wrote:
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          >>>Hi Kevin,
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          >>>Is the number of messages in the destination higher at
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          >>>If there is "very little activity" how can you
          >>>measure a slowdown?
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          >>>Can you force server side thread-dumps the next
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          >>>Tom
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          >>>Kevin Sharfman wrote:
          >>>
          >>>
          >>>>Hi,
          >>>>
          >>>>Our system makes use of queues extensively. We, pumps trhough tens
          >>>
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          >>>>of messages every day . Every few days, our Weblogic 7 SP5 JMS queue
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          >>>>with very little activity. After restarting the instance, everything
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          >>>goes back
          >>>
          >>>>to normal. We have about 14 queues in our system with a very high
          >rate
          >>>
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          >>>>Any ideas as to what slows down the queue requiring a restart.
          >>>>
          >>>>The JMS file store is excluded from anti-virus and backup software.
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Render Queue Slows Down with Large Queue

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