If you updated to version 1.06 (released September 2011), find the Game.ini file in the reconst folder, open it up, and find the line with RGSS104E.DLL. Change the 4 to a 2 and save.
Updated. Don't use the 104 file; just change the Game.ini to look for 102 instead. The 104 is the reason those weird boxes show up on the training screen.