Fraps can only record application windows that use DirectX. Which is why you can even record movies playing in Media Player and such, or games like Diablo1 (requiring directx 3), but not DOS stuff.
EDIT:
And unless you buy the full version, FRAPS only records up to 640x480 pixels of the window, starting from the top-left corner. This isn't really relevant for old DOS games that usually have 300x200, but I thought I'd mention it.
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