Spooky Slow Export Time – Any Thoughts???

I’m running Production Premium CS6 package on Windows 7, AMD Phenom IIx6, 64-bit, 16 GB RAM, with an NVIDIA GeForce GTX 560 adapter.  (I know, my adapter is no longer supported.  A real editing card is on the shopping list!)
Here’s the issue: Editing a long clip for our local church with their new video system.  They, thankfully, added another camera angle with a standard camcorder.  This was the only footage recorded for the first ½ hour of the presentation due to the fact that the operator forgot to push his/her new button.  Consequently, this is the only footage that can be utilized during that time frame.  These segments were quite grainy and treated with Video Toaster, totaling two cuts at 6 and 8 minutes apiece.  5 more cuts, ranging from 12 to 28 seconds fall later in the piece.  These were all rendered separately and as the last renders of the process.
This footage was imported at 1080p/MP4.  Footage from the church system was recorded and imported in 720p/mp4.  There is an additional clip from an existent video of 16 minutes, imported in an mov. format.  Intro and out are mov. at 15 seconds with an additional 7 second of avi cut into the intro. All, with the exception of the MOV video, are laid over an audio track in a pkf format.
Effects are limited to the Video Toaster clips mentioned and Brightness & Contrast on all except the 16 minute video.  Overall duration is 1;20;15.  All unused clips and files were discarded and I’m exporting to the Vimeo 720, 29.97 preset in Premiere.  The first export estimated at 32 hours and an immediate 2nd calculated the export at 52.  After a check and double-check, I looked to Media Encoder where I saw an estimated 17 hour export before I declined this option.  Here I cleared the Media Cache and checked export once again, estimated at 24 hours and accepted this option.  That was 37 hours ago and the encoding sequence is currently at 68% with an estimated 15;29;53 left…
What I find distressing is that an export usually runs CPU’s at 90% or above and they are currently running between 17-33% at +/- 5 GB RAM.  This will ramp up on occasion to normal levels and I’ll see the encode progress, sometimes rapidly, sometimes in spurts.
My thoughts are that I’ve overlooked something obvious and sophomoric.  Similar pieces in length of this mix-and-match type have exported in much, much less time.  Did I drop the ball by clearing the Cache?  Is it Video Toaster… Or, could it be an unknown codec from the new camera system, to which I don’t have a clue???  I doubt it, but could it be the pkf and should I have taken this to an AAC?
Thanks for any and all advice ahead of time!
~RS

Jeff,
Thanks for getting back so quick on this one.  Yes, CUDA is installed and up and running.  I didn’t import through Media Browser, but compiled all media in a folder on the desktop before beginning the project.  All auto-saves, etc., are placed here just so I don’t get things lost with projects like this.  I wouldn’t think this would slow it, but it’s a new format for me and seemed like a good idea at the time.  I’ve only done a couple other projects this way and haven’t noticed variables in speed before.  And, yes, I used “VBR 2-pass”.
Here’s a full screen shot:
Export:
The variables in this, as opposed to what I have experienced in the past, are those listed above; namely Video Toaster, but also the unknowns of the church cameras and the fact I cleared the cache.  Now, I did attempt to rerender, only to find this wasn’t necessary.
Also, it seems Video Toaster isn’t supported through CUDA as it requires full render.  Once this is rendered though, shouldn’t PP utilize this without having to re-encode?  Could this be what’s slowing the machine?  Again, my worry here is that I’ve overlooked the obvious, but I’ve been doing this quite a while… yet that’s when I seem to make the silliest mistakes!
The reason I didn't cancel this one was that I finally pulled the "go" trigger on it at 10:30pm and when I woke yesterday it was at 33%.  (Seemed a bit slow, but not overtly.)  While I was assessing the situation the CPU jumped to 90% and the "encode" bar gradually (as seemed normal) to increase to 51%.  Then, as the day progressed and up to this point, 26 hours later we, have it only at 68%.  This is a SPEC piece and I have a paying gig starting Saturday for which, I will need the machine.  My worry is that if all is working corectly and it is just being slowed by Video Toaster that I will have waisted valuable time.  The flip-side to this is obvious and that's why I finally decided to seek help here.
And, yes, I need an i7 processor but it’s great to hear your confidence in the GPU!
Thanks again!
~RS

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