I've been using AFE now for 2 years (hardly an expert, but I'll try to help) and I remember having a similar issues with very short lists of games, I fixed it reducing the maximum number of titles being displayed at one. For example - if you've got a list of 10 titles, but your layout is set to display 50 in the selection window (that's the ListTxt layer in the editor), and your selector is set to position 25 you're risking having your selector start on a blank. Reduce the maximum of titles displayed and you should be fine. You can also change your selection position (which I think will be the best solution for you) - edit the ListTxt properties of your layout - set your selection position to zero (0) or the top third of your list and your selector will always be at or near the top, not ideal but it will work and that should keep it from starting on a blank.
As to AFE not remembering your last play - that should be working - did you install the patch? Have you tried purging then rebuilding your lists (both functions are found on the Screen Options)? I find that it often clears up any list issues.
I also wanted to let you know that the English and the French (yes, I speak & read french) forums haven't been very active lately (I believe Youki's been busy being a dad) so you may not get an activation code quickly.
Havok, Youki and NoLogic are also on BYOAC - so hopefully they'll see this thread and offer a other, likely better, solutions.
I hope this helped.
WonderAlex