This is caused by the fact that your subrace bonus comes from an item you're given upon each login (as you can see in the combat window), so the single bonus spell you get will only be added about a second into play (thus losing you any spell already prepared in that slot).

This could be fixed by adding a permanent bonus/penalty to the stat (don't know if this require DM intervention?), and that also open for higher spell levels earlier (as your base stat and not buffed stat is checked towards feats and avaliable spell level) and also remove the opportunity for people to get spells they're not supposed to have, or feats they're not supposed to get ability-wise.

Con: lots of work since many PCs are subraces.

This is however, a minor inconvenience as we're talking about single spell unless you're lv 9+ and min/maxed, then its two.