Loss of stock aircraft happened to me too, after using the recommended install method (copy of a clean, patched CSF3 folder, then using multiCFS3). It is deliberate I believe, as it stops inappropriate aircraft spawning eg on airfields. Some of the stock missions are there but they are flagged 'do not fly' (because the aircraft and other items are no longer there, presumably).
I just installed the BoB alpha mod yesterday and it's impressive in many respects...
...although there are issues for me with one or two of the included 109s, including the grey square on the windshield and this:
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