ProRes 422 & Premiere Pro CS5.5.2 Playback

Question

I am a long-term user of CS5
Recently started using ProRes 422 footage, (LT in order to keep file size a little smaller). The footage is taken from a Ninja2 via the HDMI of a Sony HVR Z5.
I do a lot of post work on my projects and the native mpeg2 8 bit from the HVR would not hold out too well. Apart from that, I had no previous performance issues using mpeg 2 files.
Now the ProRes 422 footage in the preview window and in the timeline of PremPro is stuttering and won't play smoothly for more than a couple of seconds at a time. This has become progressively worse as the timeline has grown.
I use a single video track (I don't stack or nest) and often use 4-5 audio tracks ( 24bit .WAV) plus a stereo channel from the Ninja2. Audio settings within the project are 32 bit floating.
Average Data Rate of the ProRes (LT) Video File is 8.9 MB/s. Source Audio is 48KHz 16 Bit.
Edit Workstation system (exclusive, no other use):
Triple Channel 24GB 1600 RAM
i7 970 (Hex) 3.2GHz
Nvidia GeForce GTX 580
MB Gigabyte X58 (No Overclocking)
SSD OS & Programs
4 x 500 GB Sata2 Caviar Black RAID 0 media scratch disk and cache (Software RAID - no hardware controller). The RAID is striped at 128Kb.
1 x 1TB Sata2 Caviar Black project files
CPU Temps 44-46 C
System Temps 41 C
Graphics Temps 58-60 C
Disk Temps 30-40 C
The disk access times during playback are often less than 5 ms. Quick Bench (8MB zone) test gives RAID 0 Average Read Time of 642 MB/s, Random Access Time of 14 ms, and Burst Speed of 3411MB/s. CPU Utilisation is 2%. CPU system usage is fairly low as is the RAM demand with 50% often unused. 18Gb of RAM is allocated to Adobe programs (After Effects & Prem Pro) with 6GB available for other things.
I am using no external monitor interfaces.
The ProRes footage is imported into Prem Pro and the sequence setting is automatically created by dragging the ProRes file into the New Item folder.
The project sequence created by Premiere Pro is AVCHD 1080i Square Pixels 1920 x 1080, Upper Field First 25 fps (PAL) which is correct for me in the UK.
This works out fine as I have additional footage from a Sony NX5 which is AVCHD and happy with those sequence settings - I get smooth playback from the NX5 in both the preview window and the timeline. The resulting timeline bar colour is Yellow for both footage. If the Pro Res footage is rendered on the timeline (green bar) playback is fine. The render codec is by default I-Frame Only MPEG.
At the start of the project, the playback seemed fine, but now I am about 35 minutes in and the whole thing has ground to a stuttery conclusion.
The footage in the preview window scrubs and jogs fine, but plays for about a second or two then stutters, as does the timeline. I would expect my system to easily handle the Pros Res footage - but it doesn't.
Any similar experiences out there?

Answer 1

1. With that much footage, I might set previews to render to my output size, so as to cut down on final render time.
2.  112gb!  Holy Crap!  I hope you're on a fast RAID drive with that!  Otherwise saying you're headed up $*it creek without a paddle doesn't quite cover it... ...more like drowning in the $*it ocean. 
With that much information you're almost always better off utilizing a rendered file rather than relying on your dynamic link.  If playback is choppy, you need to be able to render to a drive that isn't "Busy" while you're playing from it.  I've found that using separate RAID for my main project file, and my original or AE assets allows me to render out the previews to a non-busy drive, making the output faster, and the playback faster when reading it.
Dynamic linkage is great... ...if you're going to be making more changes to that piece, leave it as is and play it back, if not, RENDER THE EFFECT, or RENDER A WORK AREA set to the clip you're editing.  If you're done for the day, render the whole damned thing and leave it until you come back.  Rendered effects will play back faster than active process effects (renders are already in the video, set into it as if native to it; active process edits aren't in the video, they are applied as it is played back, and require more processing so they slow things down), and when you come back from lunch or from home, you'll have a freshly rendered slate to preview.  This means you'll be able to show off for the client by morning.  Need a Web-capable rendering for a status update you're sending to a client, DUPE the sequence, change the preview on the DUPE to match some web capable settings with smaller frame height\width resolution and compress the hell out of it.  Youtube can play it back pretty well, and vimeo also, and you'll be able to upload it in 2-4 hours (if your system is archaic like mine, smaller video outputs great).  Personally, I've found comps with AE to be a pain when trying to link and playback.  Render a work area around the comp if you're going to play it back.  IF you want to preview a whole section, Dupe the Sequence and use the Dupe to NEST the SECTION (create a trim or edit mark at the beginning and end of the section you wish to preview, select everything between the markers, right click and select nest), and you can use AME to render a small preview file, so you don't interrupt the rest of your work.
I work with more sound quality constraint than video, and the sound quality has to be real, while the video does not need to be perfect (doesn't mean I don't damn well try; I've really just begun my journey into this world, and have only begun to use prores, but found some pitfalls to experiment and solve).  I start with whatever I'm given, go to prores, edit with a prores proxy preview at ¼ the input size, and render out once just to get started.  The effects values are applied to the preview in playback, easing the playback stutter, and allowing me to work fluidly on a laptop mac with an intel core2 2.16ghz with a geforce gfx card at 256mbvram and 4gb of system ram, with (hardware hack) 2 internal drives each at 1tb, one for main use, and one for housing my project files.  Using an old esata express card raid box, I get great speed from the playback by storing the previews on RAID, while all the other files are housed on my secondary internal drive.  With multi cam AV, you need to be able to store the main clips on different drives, or on a raid store (ideally on separate RAID stores) in order to play them back while cutting them together.  However, once cut, you should render out the preview in it's entirety, and start your other edits from that point.  Then you can render just the effects and still get great playback.
If you don't see Prores in your preview box, get the AME prores presets from the adobe site, and you can place them by hand into your app (the folder should be the EncoderPresets folder in the program files on windows, on mac open the .app by right click and select show package contents>contents folder>settings>EncoderPresets and paste the .epr files there by hand).  Then open up premiere and you should be able to use prores proxy for your previews and export.  I like to export to prores and then use handbrake to export to x264 with --fake-interlaced set up so I can use it as a transcode for Encore.  Just keep your blu-ray data rates under 35mbps and you should be fine.