slow everything, bad files were culprit, but why?

I just got a new i7 with windows 7 64 bit on it yesterday.
Everything was slow, and I figured out why, but don't really understand why, or what I can do to keep it from happening in the future.

Yesterday I attached it to an external NTFS drive that had a bunch of bad sectors, copied over vacation picture jpgs so I wouldn't lose them if the external died anymore, disconnected, and then my new baby was slow. Resource monitor had disk highest active time at 100%, any MANY processes had a disk response time in the thousands of ms (like ~14,000ms for System as it accessed one of the pictures). Many other processes that didn't access the pictures still had a disk response time in the thousands, but I'm guessing that's just a trickle down from the pictures.
I deleted the pictures and I was back up to speed, but only for about 30 seconds. Things were still slow. 100% highest active time, svchost with 11,000ms response to C:\Windows\SysWow64\KernelBase.dll. What is running 32bit? Firefox! Kill firefox, all better. Why would firefox ramp up disk time? Well, I had also emailed myself my zipped firefox profile from an xp machine. I deleted the profile from appdata, and now I'm back to full speed with firefox running.

Why would copying pictures from a damaged external cause everything to melt on a brand new hard drive? Why would emailing myself a firefox profile from an ntfs xp machine (no bad sectors) cause everything to melt? Is there an option in windows 7 file copy that doesn't copy over the crap?

EDIT: Just kidding, this isn't fixed. I'm now back to 100% highest active disk usage, but all of the processes are windows processes accessing C:\Windows\....
Now what??

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Turns out event logger shows an Ide Controller Error immediately prior to every slowdown. So either I have a hard drive that coincidentally became faulty when I copied the pictures over, or the files corrupted my hard drive. I would hope it's the former. Am I at any risk copying the files back over after I get a new hard drive from warranty?

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