I can't comment due to it being a new account, but stumbled across this whilst looking for something else and thought I'd add my solution which is similar to above and have it happen frequently when switching between docking station and laptop screen..
I have a shortcut on the desktop called fixRSAWindowPosition which calls a script with a similar name ie fixRSAWindowPosition.cmd
this contains:
@Echo Off
taskkill /im:securid.exe /f
Powershell "Set-ItemProperty -Path 'HKCU:\Software\RSA\Software Token\Desktop' -Name 'LastXPosition' -Value 0; Set-ItemProperty -Path 'HKCU:\Software\RSA\Software Token\Desktop' -Name 'LastYPosition' -Value 0
start "" "C:\Program Files (x86)\RSA SecurID Software Token\securid.exe"
I can't remember why I didn't write it all in powershell at the time, but it works for me.