You're referring to the SSD Toolbox right? I haven't tried it with RSTe myself, but if it's in RSTe passthrough mode then the native Win7 TRIM command should get through the SSD, thus you don't need to run TRIM from SSD Toolbox.
As per the http://www.intel.com/support/motherboards/server/sb/CS-033344.htm RSTe for Windows* Software User Guide, TRIM is supported in a non-RAID configuration.
Seems that Doc_SilverCreek has pointed the right direction - most likely the issue is on the embedded Microsoft NIC driver. The issue is documented in the http://download.intel.com/support/motherboards/server/s5520sc/sb/e68106012_s5520sc_msu_2010_08...
