Missing docs folder

I have a problem in OSX 10.7.2, Here is the setup:

MBP 8,1 (aka base mbp 13 of 2011 early)

Corsair F120 (divided in 3 partitions, 45gb HFS+; 45gb NTFS; 30gb ExFat)

What I did:

Moved the home folder to the Data partition (30gb ExFat) and have the libraries (windows 7) associated to the concerning folders.

Whats the Problem:

Sometimes a folder gets missing when using OSX, for example earlier at work I had tried to get to a pdf that I had opened previously, however I wasnt able to see the contents of that folder as I did 3 hours ago. I did a quick search for the pdf across that folder and the mac itself, without a success. However I was able to launch preview and get the pdf open since it was the last one that I had.

To remedy this issue I usually have to reboot the mbp.

I have run some diagnostics on the SSD to see if its dying. And it returned me as healthy, although a good deal slower (probably because of the lack of trim)

And another problem:

When I was using my external HD yesterday a strange problem aroused, finder couldnt copy the file that I sent it to, since this is normal in my problematic usb ports, I did what I needed, which was to kill the unresponsive finder and to reboot the mbp. However now when I insert any external HD, Im faced with a finder that force quits and relaunches, continuously without an end.

Thanks for all the help!!