If LCD is active the CRT will always output 1024x768 (or whatever is the _physical_ LCD size) and smaller modes are zoomed to fit on the LCD unless you specify Option "lcd_center" in the device section.
The pixel clock for this physical size (e.g. 1024x768) mode...
If LCD is _not_ active, the normal mode lines and pixel clocks are used for the VGA output.
Whenever you switch output sources with Fn-F5, the Xserver won't get informed and pixel clock and other settings are wrong. Because of this you have to switch modes _after_ switch output sources! Then the server will check which outputs are active and select the correct clocks etc. So the recommended key sequence to switch output is
Fn-F5 Ctrl-Alt-Plus Ctrl-Alt-Minus
and everything should be ok..
on the Toshiba keypad you can first hold down Ctrl-Alt, then press `Fn' additionally before pressing Plus/Minus too to avoid to explicitly enable/disable the numeric keypad for mode switching.