Sounds like WB hit the nail with "Use those knobs and buttons of your monitor to move/resize the screen."
Here's the long explanation ...... (I have no idea how liquid displays work - they will probably be the same as below, but that's a guess)
CRT monitors often (usually) need to be tuned up for each video mode they have to display, especially when they use different refresh rates. When you switch fullscreen this is what is probably happening - the game/app may be trying to do fullscreen 320X240 @60Hz (or whatever), and your monitor needs to be adjusted to cope with that particular resolution/refresh rates.
Try this. Start Dosbox up and fire up the application that is missing the bottom of the screen.
Use your monitor adjustment buttons to fit it on screen - don't worry - monitors mostly remember these new settings on a per resolution/refresh rate basis, so you shouldn't be screwing up your normal view. ( If you have a really old CRT monitor then you may have little screen tuning wheels instead that remember nothing, bu they are fast to readjust.)
When your troublesome app fits in the screen, try Alt+Enter to switch it back to a window to make sure all is well.
You may have to do this a few times with fullscreen apps but most monitors released in the past few(lot) of years will remember each video mods settings and switch automatically when an app changes resolution/refresh rates.
Did this hep at all?