IMO, there is no way that this could come from a problem in VBA or the ROM (if something was really wrong in VBA or the rom, you would have a ton of bugs, not only a 'one bit' problem...).
So it looks like you used cheat codes to me (or that you used a save from someone that hacked the game). The 'pokemon' option in the menu is just a 'on/off' bit to set, and if it hasn't been set on by the game for some reasons (like if you never finished the event that should enable it), or if it has been set off by a cheatcode (or by editing the game's ram manually), you get this 'bug'.
So my advice would be to go back to your hometown, and to try to finish the event that should turn this bit on (ie., if clements is right, see if the professor is still offering you a starter pokemon). If that doesn't work you have to find which bit to set on manually (I can't help you on this one), or find on the web a code that enables all the menu's options (it should also re-enable the pokemon menu) (if such code exists).
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