[Joe Sr.]

Moving away from the software question (though I will add that I, too, like Beersmith) it sounds like you fermented for two weeks and then racked to a secondary where fermentation continued prior to packaging.

If that's the case, you simply racked before fermentation was complete.  Rather than try to stick to a set fermentation schedule you should let the beer ferment until it is complete.  In this case, maybe start taking gravity readings at two weeks and package when it is stable.  It's stable when it's stable, whether or not that matches the initial prediction.

There is no real need to rack to a secondary and many of us regularly do not.  There are reasons to do so (dry hopping, add fruit, bulk aging, etc) but in most cases it is unnecessary.  My beers typically sit in primary for about four weeks and then go straight to the keg.

[ynotbrusum]

And remember to calibrate your hydrometers.  I kept getting consistently low numbers by a few points to a couple points.  I have two hydrometers - one is spot on and guess what?  The second is low by 2 points (reads distilled water 2 points low at 60F.). I now have that one marked with a permanent marker.  And my estimates are much closer, though still not always what the program predicts!  I go by taste, rather than numbers much anymore, since I brew pretty light lagers mostly. 

[Jeff M]

Have you determined your systems effieceny and changed it in beersmith?  This could be why your high?  As for fermenting lower then expected, your MLT might have temperature irregularities which is causing you to get a different sugar profile then expected.

Ive never really understood attenuation even tho i have read quite a bit on.  I was always under the impression from the wine and mead making i have done that yeast will eat any ferment-able sugars available, and you probably wont stop them;)