The MCE IR codes are a form of RC6 mode 6A. It does include a toggle bit.

If the Pronto does not correctly process the toggle bit, AND the device does not have the registry entry for disabling that feature, then using the same key twice in a row would fail.

I don't recall whether there are any models of Pronto that correctly process the toggle bit for MCE. Most or all models of Pronto can correctly process the toggle bit for RC6 mode 0 (normally just called "RC6"). But this is not the same thing. Some versions of ProntoEdit understand a special condensed form of Pronto Hex for RC6 mode 6a, but even in that form they don't get the toggle bit right.