Will changes in Premiere timeline affect AME during background encode?

If I am doing a background encoding of a timeline in AME while continuing work on that same timeline in Premiere, or Audition, will AME reflect those downstream changes (obviously not the ones it has already "printed" as output) or is it "locked" to the version when I first sent it to AME?
And:
Should I be making changes to a timeline that is also being background encoded in AME?

See this:
http://blogs.adobe.com/aftereffects/2011/06/adobe-media-encoder-project-version.html

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Premiere CC to AME - H.264 nightmare rendering problems with CUDA on rMBP

I've been struggling for weeks trying to troubleshoot and narrow down my encoding nightmare on my own and I have finally succumbed to getting the forum's or Adobe's Help.
Problem:
Rendering a Premiere Pro CC project with via Export Media > Queue to AME in H.264 causes the encode to randomly fail on multiple projects.
I find it quite amazing that this error happens as I surely am not the only one rendering ProRes to H.264 on a new Macbook Pro!
Symptom:
Output preview starts to flicker then encoding stops randomly, preview window turns to a black screen or simply stalls while the Elapsed Time keeps rolling, PProheadless crashes in Console, encoding sometimes resumes after several minutes post the crash (but sometimes not) however the final output in such case is garbled before/after the crash. Computer is useable. All other software shutdown. Not using computer during encode. Can reproduce virtually every time.
Hardware:
Early 2013 Retina Macbook Pro
Processor 2.8 GHz Intel Core i7
Memory 16 GB 1600 MHz DDR3
Graphics NVIDIA GeForce GT 650M 1024 MB
Software:
Premiere 7.0.1 (105)
Adobe Media Encoder 7.0.1.58 (64bit)
Creative Cloud Latest Updates
Cuda 5.5.25 (latest)
GPU Driver: 8.12.47 310.40.00.05f01
OS X 10.8.4 (latest)
Project Details:
ProRes 4:2:2 or AVCHD sources
No nested sequences
Video track with image over whole sequence
Video track with text over whole sequence
Video track
Audio track
Sometimes video track with adjustment layer
Standard disolve effects between cuts
4 effects used: denoiser for audio, luma corrector and twice Fast Color Corrector
No third party plugins installed nor used
Sequence is set to Maximum Bit Depth / Max Render Quality / Linear Color
Use Previews off
Encode is set to Maximum Render Quality and always H.264 2pass VBR.
Errors in console:
8/27/13 12:38:01.144 AM PProHeadless[1389]: [CL_INVALID_OPERATION] : OpenCL Error : Failed to retrieve device information! Invalid enumerated value!
This is seen at multiple times while starting Premiere (no crash) and while starting the encodes and usually after/during the crash.
Crash report:
Process:         PProHeadless [410]
Path:            /Applications/Adobe Premiere Pro CC/Adobe Premiere Pro CC.app/Contents/PProHeadless.app/Contents/MacOS/PProHeadless
Identifier:      PProHeadless
Version:         7.0.1 (7.0.1.105)
Code Type:       X86-64 (Native)
Parent Process: dynamiclinkmanager [397]
User ID:         501
Date/Time:       2013-08-26 21:12:21.878 +0200
OS Version:      Mac OS X 10.8.4 (12E55)
Report Version: 10
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGSEGV)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Full Crash report:
http://pastebin.com/a93cNVqk
Attempts to solve the issue:
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Tried encoding with source on internal HDD, output internal HDD, source exterbak RAID, output internal HDD
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Uninstalled other software that could mess with the graphics: Colormunki, Parallels.
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Encoding directly via Export Media > Export without Queuing to Adobe Media Encoder seems to work fine. I have not tried this too many times because I need to render multiple outputs and doing it without AME means a lot of 'sitting and waiting' to click Export for the next format. This is not an option.
Tried deleting the Media Cache
Completely reinstalled OS X 10.8.4 from scratch with no other software running and tried to export. Same problem.
Performed Apple hardward test. No problems.
To Test:
I'm planning on installing Bootcamp so I can test the problem in the Windows version and I could pinpoint it to a hardware problem rather than a software problem.
Notes:
Problem happens with CUDA and Open CL modes although in Open CL mode, the whole computer tends to freeze intead of just 'stalling'.
Editing and playback inside Premiere is OK! Even encoding out of Premiere is OK directly but not useful for me as I need to render each project to 5 different H.264 formats.
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I've submitted a bug report but their reply is not very comforting:
but their bug report says "Due to the volume of submissions we receive, responses to inquiries are generally not possible. However, we may contact you if we need clarification on your submission." Nice.

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Hunt

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Will changes in Premiere timeline affect AME during background encode?

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