New-ish Macbook booting/running extremely slow after 10.6.3?

Question

Hi all,
I bought a refurbished Macbook in March 2010. A few days ago I installed the big updates along with 10.6.3 and everything was fine. I was then trying to play an .avi with VLC media player with some other programs open (Firefox, iTunes I think). VLC started not responding along with the other programs and I got the spinning wheel for a little while. Eventually I forced quit everything and restarted. Upon this restart (and, incidentally, this would have been the first restart after the initial install/restart of the above updates) my Macbook was running really slowly. Extremely long boot up times (like 10-15 minutes), constant spinning wheel in OS X (takes about 1-2 minutes to load the system drop-down menu, longer for apps like disk utility). Everything runs fine, just massive load times and spinning wheels when doing anything.
I hadn't installed any new programs, widgets or any other stuff aside from the update last week.
The laptop's memory usage seems pretty normal (about 1.2/2.0gb free RAM, no page-outs) and nothing seems to be bogging down the CPU. All my processes are Intel. I have about 40gb free on my 120gb hard drive. Checked my Font Book and I have no duplicates.
I tried resetting PRAM (no change) and I verified/repaired the disk with DU (no trouble found).
I ran the Apple Hardware Test and everything came up without problems.
I ran repair permissions from the OS X CD and it repaired a whole bunch of Airport stuff and I got a ton of "Open Error 1" for keyedobjects, etc but the latter is normal?
What should I do next to resolve this? Is it an Airport issue given the repaired permissions? I'm guessing it's likely software/update related, since all my hardware SEEMS fine... Any help would be very much appreciated. Please let me know if you need more info.

Answer 1

Hi again.
So after my above fiasco I decided to completely reformat (zero-out-data) my drive and do a clean install. After doing this, I began reinstalling all my previous software, and everything was back to normal, very fast, smooth, etc.
Today I decided I'd grab all my music and other files over from my PC's external hard drive to put it on my Macbook. I copied all my separate, misc. files like photos and .psd files and text documents first (about 5gb), and then copied my music folder next (70gb or so). After copying exactly 48gb, the computer froze and I got a spinning wheel. I couldn't click the X to stop the transfer and I let it sit for a good 30 minutes spinning away before trying force quit, and Ctrl - Option - Command - Eject to restart. Nothing worked. Eventually I just gave up and held down the power button.
Macbook restarted fine but then trying to resume the transfer of the rest of my music files kept giving me errors. The first time it copied an album or two and then hung up, this time allowing me to hit the X on the transfer. I tried one more time but it hung up after the first file, and more spinning wheel. Again, the computer was completely unresponsive with the spinning wheel, so I was forced to power button.
Now I get a similar experience to the first time (OP comments), but the start up is much faster. Still spinning wheels, but not as frequent. More importantly, I can't move any data currently on my macbook back off of it, using FAT32 USB sticks or anything. I tried once but I got another transfer hang-up so I don't want to try again. I can hear the hard drive "slip" or whatever, when I try, and then it just churns and spins around trying to find itself. I get similar sounds on start up, but eventually it seems to kick in and be fine.
(For the record, I had this same inability to write data from my macbook the first time this happened.)
Is this just because I had to force shut down the computer? Again, the computer was running fine until the freeze-up + force shut down.
Is it possible that the files I'm copying over were the cause? I had copied the same files over from the same NTFS hard drive right when I got the computer back in March, and they were working fine on the Macbook up until the first issues started a few weeks ago.
It seems to me like a hard drive issue, but Repair and Verify still comes up clean.
Thanks in advance!