I have an EVGA SR2 build with two Intel Xeon X5680, 48GB ram OCZ Reaper HPC Series at 1600 MHz running on Windows 7 x64 Proffesional. My bootable hard drive is an OCZ Vertex II 120GB and I have an extra of 4x1.5TB Seagate Baracuda. I am a web-developer/designer myself so I do a heavy multitask with many apps open 24/7. Now, all my apps are installed on one of the Seagate hard drive and my important source files are on another Vertex II 60GB (6th hard drive).
When I work with my source files, if I leave the PC idle for some period of time and I get back to it, on the next save it takes 6-7 seconds to load the explorer (does that makes sense?) and during that time it shows the loading icon:

Also when I try to open my files it does the same, or open an image... Mostly this happens when I try to search something from the start button... It seems that files or not cached? I don't know to explain this.
The CPU usage is never more than 2% and the memory around 5GB out of 48GB.
Anyone had this problem before? How can I solve this? I never had any problem on any other PC in the past and the files are being saved on an SSD so I can't see why it takes so long?