Entire project broken somehow! AE, ME and PP

Hello everyone
I've come here as a last resort to my project being broken (yet again!)
Symptoms include:
Premiere Pro:
all media is pending, on start-up it's loading each file very, very slow (7MB/s maximum in Disk Monitor) and after an hour or two when everything is supposedly loaded by PP, it still shows Media Pending on the monitor.
After Effects:
The AE project which includes the Dynamically Linked sequence from PP crashes on start-up. Nothing I can even do about it in AE.
ME:
I can open the AE project but it shows no compositions available for rendering. Just a blank column.
What I have tried so far:
- Cleaned the media cache
- Manually deleted the media cache
- Defragmented the HD
- Checked SMART and other self tests on the hard drive. The drive is in perfect shape.
- Added exception rules for all *.exe's I could possibly think of that are related. (dynamiclinkmanager, QTsomethingserver, PProheadless, AE.exe, PP.exe, etc)
I will try updating everything to the latest version now but I don't believe this will work as I have had this problem before with a fully updated CS.
The last time I had this problem (about a week ago), I managed to fix it by re-installing the entire CS5.5 Master Collection. I do not want to do this again as I'm using a (volume?) license from school which requires me to physically bring my computer in and let them enter the serial. (Is this even normal that I do not receive the license I've paid for?)
I am really lost right now!
Regards

I appreciate the reply Harm but unfortunately it's not helping me much. As I mentioned, I'm still in school and I can not really afford a dedicated editing station, especially when I'm not headed in this direction of media development Of course you made a fair point and I apologize for forgetting the basics of a post like this.
I'm running a Windows7 64- i7 2500K overclocked to 4.5GHz with 8GB of DDR3. My main disk is a Vertex2 SSD and my storage HD (Media Cache, applications) is a Samsung 2TB 7.2K RPM SATA2 disk Perhaps you are mixing up Mb and MB because 7MB is not OK at all for a hard drive like this. It should be getting atleast 100MB in read (140MB average as confirmed on other tests.)
My other projects are working fine, so the hardware is excluded from the source of the problem.
I would like to add that I have just updated my CS5.5 to its latest versions, renamed my source files folder and the problem persists. Extremely slow reading speeds of footage after I have re-located the file in the popup window that came up after it couldn't find the clip in the original location. I believe this is what causing AE to crash: it can't read the linked sequence fast enough and AE times out.
I apologize for my bad writing skills, English is not my main tongue
Regards
Message was edited by: Pieterjan - KL
I forgot to mention that both times this happened, this was after I nearly finished my project and I was rendering the project in Media Encoder. I don't risk to experiment anymore but I believe this happened when I canceled a render in ME. Perhaps I have found a bug? In the meanwhile, it has suddenly decided to work again. So I'm finishing and rendering the project so I will not have to touch it ever again.

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