Premiere has slowed to a crawl. Please Help

Question

Hi, I am a photographer and video editor. I built my computer about 15 months ago to work with CS5 and the Mecury Playback Engine. In the past few months it has been slowing down at an alarming rate. Over the holidays I created a video montage of pictures from my brother's wedding and Premiere kept stopping with an error that read something like 'Open GL driver failed' adding something about 'lack of memory'. I had to switch to software mode and avoid playing the timeline (to avoid rendering each photo, there were well over 100) so I could finish it in time. And now a project I am getting paid for will no longer play back smoothly. I get about 1 second of smooth video before it starts jumping and freezing all together. The audio continues but the picture does not. Here's what I have.
Intel Core i7 950 (quad core) 3.07GHz
12.0 GB Ram
Windows 7 Pro 64bit SP1 fully updated
Nvidia GTX 470 w/ 1280 MB GDDR5
     current driver. 285.62
C: 60GB SSD for system and programs 4.64GB free
E: 300GB 10000 rpm 16MB cache VeliciRaptor Drive for Project files preview files/scratch disks and such 134GB free
G: 1TB 7200 rpm 32MB cache Barracuda Drive for Assets 158GB Free
I have 2 other drives but they are not used in this workflow.
Page file = 36859MB automatically managed on drives C:, E:, and G:
My Power Usage plan is set to High Performance.
I am editing in Premiere Pro CS5.5.2 (003 (MC: 258762))
The programs I have running in the background are: Realtek HD Audio Manager, NVIDIA Settings, Zone Alarm (security), Dropbox 1.1.45, Spyder3Utility, and as of today Spybot.
The Project is a short 10-12 min Documentary type video. It's mostly interview footage with various B-roll interspersed. The main timeline I use is 4 video and 4 audio layers. The fourth layer in both is turned off to holding stuff. There is not much in them. Layer 1 is pieces of another timeline. That timeline consists of 2 layers of interview footage from 2 angles with a third audio track from the zoom recorder all synced and color corrected. I adjust opacity here to pick which camera angle to use, but cut this timeline together in my main timeline to minimize sync problems and added color correction steps.  In the main timeline, video layers 2 and 3 are B-roll. audio layers 2 and 3 include one short sound effect and a few pieces of music. Some of the music has been slowed or sped up to fit the timing needed. Premiere quickly renders that sound when I start up the project or make changes to those files in the timeline.
All audio is either MP3 or WAV files.
Most of the video is Canon DSLR footage (5D mkII, 7D, and 60D I believe). All 1920x1080 30p (a couple 24p by accident) there are some Jpegs, TIFFs, and one PNG file. Many of the pictures are housed in sub timelines with 2 layers. one with a moving picture and the other with a Gaussian blurred version in the background to fill the frame. There are some timelapeses that are of various sizes but nothing smaller than full HD. 2 are MP4 videos and the rest are quicktime.
All my timelines are preset for DSLR footage at 1920x1080 30fps.
Almost the entirety of my timeline has the little yellow line over it indicating that we should be hardware rendering this footage.
A few things about how I have worked with this computer. I built it for CS5. When I first started using it, it was brilliant. Lately The whole computer has slowed, a lot. last week I uninstalled some extraneous programs and tweaked somethings. Most everything on the computer is now running back up to snuff. Premiere is not. It is too the point that I cannot edit and a new edit of the project is due this Friday. When I first started using this computer I got some noise from the GPU and CPU fans when I would load up a heavy duty project. That made sense it was making the computer work. Now I get almost no noise from either fan and the thing runs like crap when I am editing. This doesn't make sense to me. Has something changed with an update of Premiere that changes the way it leverages the hardware, cause I doesn't seem to be doing that at all. Or might I have unknowingly flipped a switch somewhere that changed that leverage. In the Project Settings the Video Rendering and Playback is still set to Mercury Playback Engine GPU Accelerated. On the same line I have noticed much less fan noise when rendering with Media Encoder. I can't say I've seen a huge hit in performance there, but it doesn't seem to be taxing the GPU like it used to.
Please help if you can. I don't have time in my life to start the computer over with a fresh install on windows. Thanks so much.
Michael

Answer 1

I see nobody has suggested you delete your preferences.  I do that whenever any app, not just Pr, starts acting strangely.  I think with Pr on Windows you launch with the shift key held down.  If that's wrong, somebody please correct me.  I use a program on Mac called Preference Manager to keep good copies of preferences, because they get corrupted so easily on FCP especially, and also Ae.
Here's another general rule I employ, when Pr (or any NLE) starts behaving badly.  It could be you have some corrupt media, which will cause your app to hang or quit, which you haven't described, but I suppose it could just bog things down.
Load a totally different project with totally different media.  Does Pr work fine now?  If so, your problem project may be corrupted, or it may contain corrupt media.
Make four copies of your sequence.  Delete all but the first 1/4 of your sequence in the first copy.  Now, does Pr work better?  If so, great!  You've just determined the issue is in the last 3/4 of your sequence. 
Now, delete the first quarter, and last half from the second copy.  And so on.  Repeat this until you've found the section that causes your problem.  Then subdivide that section until you've isolated the problem footage.  Remove or replace that footage item with a non-corrupt version.  Or, learn to live without it, or try transcoding it to another format, etc.
You also mentioned that you're using Nested Sequences, right?  These have been a problem for me in a few projects, mostly with exporting, but worth a shot maybe:  Render out the nested sequences to a lightly or uncompressed codec, and replace the nested sequences with the rendered file. 
This is a long shot, but hey, you've got to start using the process of elimination to get to the root of your problem.
If Pr works lousy no matter what project or footage you load, that suggests there's something wrong with the install of Pr, or some other OS, virus, hardware or driver related issue.
I'm throwing a lot of ideas out there, and here are some more: 
Open your Task Manager, and rig it so you can see the CPU performance.  Are your meters clipping, or running at full bore?  If so, your CPU may be having trouble keeping up with all the Long-GOP decoding you have going on.
Transcode your MP3 to WAV, and replace in the Timeline. 
Transcode your Long-GOP material to an intraframe codec, and replace.  A lot of Windows users use Cineform.
I'm fixating on your remark that when you started, things were "brilliant," but have since bogged down.  That's why I was thinking VM, and also I can see how your continuously adding elements to the Sequence are slowly causing more challenges for the CPU and GPU.
I'm looking forward to your fixing this, and letting us know how you did it.