Premiere Pro freezes in render. Frame count looses sync with timeline.

Hey Guys!
I'm completely baffled by this. So I really hope yall can help. Here's what's going on.
I'm rendering a somewhat lenghty sequence (26min) in Permiere Pro CS6 that has much of the usual going on. (Color Correction, image tweeks, ect. - nothing fancy) I've finished this edit and wanted to export it to a ProRes file. Sent it to AME and hit render with my normal 1080p, quicktime, 29.975, prores settings and about 1 min into it the time shot straight out of the park. (I'm talking like 104+ hours at one point) I checked my settings and tried other export options, still acting wonky. I even tried removing all effects and export the normal sequence sans frills. Na Da. Then I thought, "You know what, maybe it's just a weird part and it'll pass through it." Nope. Left it going for about 13 hrs and it was moving so slow I thought it was frozen.
Here's where the odd discovery comes in. I decided to render the work area of my timeline in an attempt to narrow down the problem and bingo. When I started the render here I was able to view the frame count along with the video clip progression via the number and red line that becomes green. What I discovered is that in the first clip that's roughly 4 sec (should be about 120 frames) it regestered over 800 frames before it moved onto the next clip! The timeline does not reflect these phantom frames at all. However, the renderer sees the total number of frames for the sequence correctly at around 46,000 frames. It seems as though the frame/clip sync gets so far out of wack that the renderer gets exponentially lost. That would explain why the longer it works, the slower it becomes.
I'm really not sure what's happening. I feel really out of my depth here. lol Any help you guys can give me will be greatly appreciated!
Thanks!!
Parker

Mark - thanks for your reply. Disabled GPU acceleration and try software mode. Started rendering but super slow and also lost all my previews.
Here is my system:
Macbook Pro - late 2011
Processor - 2.5 GHz, Intel Core i7
Memory - 8GB 1333 MHz DDR3 (still have close to 4GB free)
Graphics - AMD Radeon HD 6770M 1024 MB
Software - OSX 10.9.1
I have one sequence (less than 5 minutes) with several backgrounds and one lower third .mov playing. I am using green and ultra keys.
Really appreciate your help. Everything worked fine until the latest Adobe Pr update. Was working fine even after update Mac software to Mavericks.

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