Solid State Drive Occasionally Freezes For A Minute While OS Is "Beach Balling"
This could have to do with power management, trying to disable the SSD from time to time to spare some power which is probably not the best idea if it doesn't work out the way it should. I think this is because this was an improper installation (you cloned the data instead of reinstalling) and hence some setting is not set properly for your SSD, it could be that this is configurable in the power options but here's a more generic approach that has shown to work across various SSDs (mostly Crucial / OCZ) and even worked for the Intel 330 series in two foreign topics.
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStor\Parameters\Port0]
"LPM"=dword:00000000
"LPMDSTATE"=dword:00000000
"DIPM"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStor\Parameters\Port1]
"LPM"=dword:00000000
"LPMDSTATE"=dword:00000000
"DIPM"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStor\Parameters\Port2]
"LPM"=dword:00000000
"LPMDSTATE"=dword:00000000
"DIPM"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStor\Parameters\Port3]
"LPM"=dword:00000000
"LPMDSTATE"=dword:00000000
"DIPM"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStor\Parameters\Port4]
"LPM"=dword:00000000
"LPMDSTATE"=dword:00000000
"DIPM"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStor\Parameters\Port5]
"LPM"=dword:00000000
"LPMDSTATE"=dword:00000000
"DIPM"=dword:00000000
Save this as a .reg file and execute it, then reboot so the driver loads it. Make sure you run the latest RST / AHCI drivers for these settings to be applied, and that you don't run the default MS drivers for that. Make also sure that any other drivers for your system are up-to-date...
When you are unsure, feel free to back-up HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStor\Parameters first.
Good luck!
Sources:
http://geekmontage.com/texts/ocz-vertex-3-freezes-locks-up-stutters-and-crashes/
http://forum.crucial.com/t5/Solid-State-Drives-SSD/Solution-C300-Disk-Freeze-ups-in-Windows-7-solved-for-me/td-p/38766
http://www.ocztechnologyforum.com/forum/archive/index.php/t-91023.html?s=c98e6645624ba3eaa4cb30e049d54929
http://communities.intel.com/thread/22483
http://geekschat.net/threads/ssd-freezing-pausing-issue-how-to-fix-it-if-you-are-using-intel-lpm-feature-we-hope.3059/
http://forum.corsair.com/v3/showthread.php?t=96663
http://windows7forums.com/windows-7-hardware/69796-intermittent-ssd-freezing-newer-laptops.html
http://www.overclock.net/t/1103319/ssd-general-information-compilation
Reported fixed on Intel 330:
http://forum.benchmark.rs/archive/index.php/t-283887.html
http://bbs.kakaku.com/bbs/K0000362037/SortID=14625846/
Reported fixed on other Intel SSDs:
http://communities.intel.com/thread/26374
http://martinlutonsky.com/blog/?12-lenovo-thinkpad-r61-a-ssd-intel-520-120gb
I've managed to eliminate similar problem by switching SATA controller from AHCI to IDE mode in boot setup.
It is not trivial - OS won't boot after the change. Check out this question: Change from IDE to AHCI after installing Windows 8