xte uses the XTest Extension, and just adds your requests to the current modifier state, rather than trying to start from some base state. Other tools such as xdotool provide a --clearmodifiers option, for example, to ensure you will get exactly what you want.
Since xbindkeys notices your request when the modifier state is with Shift_L or Shift_R pressed, this is the state xte works from. You should be able to emulate a shift-up to cancel this in xte by starting with keyup Shift_L, and perhaps also Shift_R. The real shift-up later will be ignored, or you could restore the shift state to what it was at the end of your xte actions, to avoid the need to press the shift key again, but that is for you to choose.