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I have an Acer Aspire 3000. Here for specs:
http://reviews.cnet.com/laptops/acer-aspire-3000/4505-3121_7-31532504.html

One day whenever the thing would boot up it would get to the main windows screen then
the keyboard and mouse would just get extremely sluggish. (To the point where
one mouse move took minutes). Then everything would lock up. I booted with
Knoppix live cd to pull out some files that I needed and then I used the system recovery disk that came with the computer to nuke and restart.
It only reformated the C drive (I had the HD partitioned into c and d) and then when
the setup windows screens came up it everything locked up again. The only thing
I can think of is that what ever is causing the problem (virus? malware?) is on
the D portion of the drive. When I boot with Knoppix the keyboard and mouse work fine.

What are my options here? Can I use the knoppix to reformat d in FAT32 or NTFS then go redo the system restore? (I'm not too familiar with linux. This live cd was suggested to me as a way to go in and rescue data).
 

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Believe it or not, video drivers can cause mouse issues. Do you have the latest drivers for your video. You can also test to see if it's a video issue lowering hardware acceleration on the video card
This may take a while. Right click on desktop>properties>settings>advanced>troubleshoot tab at top. Now lower the slider one notch and click ok until out of the windows. You may have to reboot. Test and see if it helps, if it does then it's probably a driver issue.
 
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