Can't render in Premiere when I have After Effects open MAC OSX YOSEMITE

When I'm using dynamic link with AE files in my PP timeline I can't get it to render at a normal pace. It will start and then crawl for the simplest of tasks. The only way I get it to work is by clicking off of PP into AE and then back to PP again. Then all of the sudden it renders in seconds. Sometimes I can't even get it to playback at 1/4 quality unless I click off from PP to AE to PP again. The tasks I'm talking about are fairly simple as well. Something like a lower third graphic/text.
At work, I'm using an iMac 2013 3.5GHZ 32GB Ram Nvidia 780 4GB with the latest version of Yosemite 10.10.2.
I connect a USB 3.0 external hard drive dock and 2 3TB Western Digital Red drives formatted in NTFS using Paragon NTFS to access read and write. Using the Mac's internal SSD for scratch tracks.
This isn't a new issue for me...This has been happening for about 6 months. Was hoping updates would solve it but it doesn't see like it's being addressed. I'm assuming it's a Mac issue because this doesn't happen to my PC at home. Does anyone have any insight into this? Is this a known issue?
PP 2014.2 Release
8.2.0(65)Build
AE 2014.2 Release
13.2.0.49

Hi Tom,
Thanks for responding.
Media is on an external drive (firewire 800)
I've tried again and found that if I wait about 1-2 minutes after the save bar locks at about 90%, the project does eventually save.
If I then quit out of Adobe Media Encoder, it still takes quite a long time to save, but somewhat shorter.
If I then quit out of Premiere Pro and relaunch, everything gets saved quickly, normally.
Like I said above, this seems to happen only after I've cued something out to Adobe Media Encoder.
Otherwise, things appear to be OK.
david

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