Exporting to Media Encoder and file locating issue

Question

Ok, Now I've read a LOT of threads trying to find a solution to this but none of them have answered my problem exactly, so here's what I have:
Running a New computer with a clean install of Windows 7 64 bit and Adobe CS4 Master Suite
Hardware:
Dell Precision M6400
Intel(R) Core(TM)2 Duo CPU  T9900 @ 3.06 Ghz, 3.07 Ghz
12.0 GB Ram
Premiere ran fine for a while, but soon I've run into a problem where I try to export to the Media Encoder and I keep getting the error:
"Could not read from the source. Please check if it has moved or been deleted"  over and over
I have deleted recently imported media one at a time to try and locate what's causing it since it wasn't doing this before, but no luck.  So I restarted the program but now the Premiere project won't open.  The task bar loads until about 2/3 in and stops there indefinitely, I've left and came back to it 2 hours later and it hadn't moved.  I back tracked and found a previous save that will open, but it still will not export, it still says "Could not read from the source. Please check if it has moved or been deleted".  And as soon as I update anything and save a new file that one will not open either.
I've tried recompressing each video file into a format I know works well with Premiere but still no difference. 
This problem has plagued my workflow for a while now and I can't take it anymore.  I've had to restart clean project files to try to work around it but I lose so much progress, and the work around by rendering the premiere file through After effects hasn't worked either.  The error I get there says "Dynamic link server is busy".
Here's what the problem is not:  It is not because I uninstalled CS3 or any other previous version, I've never had it on this computer.  It's not a plugin problem, I don't have any plugins on this install except for the default ones that Came with Adobe Master Suite for Premiere Pro. 
Someone please help me, this is ridiculous that I have had to trouble shoot the program this much.  Both CS4 and Windows 7 have been around for over a year now and neither are in Beta Editions

Answer 1

Wow, sorry, forgive me if I've seen most forums work with a lot less, and your dismissiveness led me to assume you hadn't read my post.
All of this is new and up do date as far as Adobe and Windows updates go, that's Version 4.2.1.
My projects for this are all in NTSC Widescreen DV 24P, the particular sequence that I render from is in that format as well, although regardless of which one I use the problem keeps occurring. 
My renders for my recent purposes have been compressed in .h264, IPOD video Large.  The codec I'm rendering in also doesn't seem to matter, because I've tried this in .avi., .mov, .h264, .wav, etc. and all with various settings that I thought might help, but the encoder quits encoding 4 seconds in and gives me the error that it can't find the media.
And I didn't mention the media type and what not because it seems irrelevent of what I use this problem keeps happening.  I'm pretty sure it's a problem with the project file or perhaps the media encoder or both.
And I don't know what you mean by "disks"
Do I have a Raid set up on my hard disk?  No, I have two 0.5 TB hard drives, Programs on one (C:\) Projects on the other (D:\). 
What address am I saving the scratch disks to?  I use the default of "same as Project".  Have I tried Clearing it?  Yes.
I don't think I'm getting at what you're asking.
And I don't think I've ever used an .xlsm (which is excel?) file and I've definitely never used a Power point project (PPS?) file in my projects.  And they open in their respective programs, although I'm not sure why you asked about that.  Again I'm not sure I know what you mean.
The Premiere Project (.prproj) file is what I'm trying to open when the progress bar stops at 2/3 the way through and forces me to terminate the process with the task manager to close it.
It would help to mention that all my projects are animated and I use premiere to cobble them together, so no problems that relate to transferring media from a camera to the computer would apply here.  Most of the files I get out of Maya are in Default .avi or .mov files, and I also use a handful of .wav files for the dialogue and .jpgs for cards and placeholders. 
I believe that this problem began when I updated a few of the files in my project, but I've been doing that for weeks without incident.  I've been updating them by saving over the old media file with the updated one of the same name, length, and type. 
I don't work exclusively with Premiere, in fact it's not what I usually use, that would be Final Cut Pro.