When switching from a X virtual terminal (VT) to another VT using Ctrl-Alt-Fx while the VBoxSDL window has the input focus, the guest will receive Ctrl and Alt keypress events without receiving the corresponding key release events. This is an architectural limitation of Linux. In order to reset the modifier keys, it is possible to send SIGUSR1 to the VBoxSDL main thread (first entry in the ps list). For example, when switching away to another VT and saving the virtual machine from this terminal, the following sequence can be used to make sure the VM is not saved with stuck modifiers:

kill -usr1 <pid>
VBoxManage controlvm "Windows 2000" savestate