Hi! Sorry, I did not follow this thread from the beginning, and maybe this has already been proposed or ruled out, but could it be a problem with your graphics card? I had the "square white box cursor" problem once on an ELSA Winner 1000 T3D and got rid of it by disabling the hardware cursor. Appropriate section of XF86Config follows below, note the 'option "sw_cursor"' line.
Hoping on the slight chance that this might help, Manuel ---XF86Config Section "Device" Identifier "Elsa Winner T3D" VendorName "Unknown" BoardName "Unknown" VideoRam 8192 ChipId 0x8a10 Option "sw_cursor" # Insert Clocks lines here if appropriate EndSection