We have been having this problem and wtih the help of support have tracked the issue down to Flash redirection. If you turn off the EOP option it no longer happens.
I'm using Thinshell installed in Windows 7 and I connect in my Windows 7 VDI. Sometimes (8 or 10 times per day) the keyboard doesn't work properly, operates as if the "shift" key was pressed down.  When that is happening, if I disconnect the session  and reconnect, everythink starts to work ok again.  Could you help me?
keyboard desconfiguration