What version of FFMS2 are you using? Current FFmpeg versions have a broken version of a function used to determine the "best" (least lossy) colorspace to convert to, and the Fraps decoder uses the somewhat unusual and deprecated pixel format YUVJ420P (which in Avisynth terms translates to fullrange I420), so it's entirely possible that something goes wrong during the output format decision and FFMS2 decides to output RGB instead. Very recent FFMS2 beta builds have a workaround for this bug, so try that if you haven't already.
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