Hi Thomas,
Congrats on your new baby. Once your through the teething stage I know that you will have tremendous blessings from your board.
To address your questions -
Registrations - Yes what has been said already is what I do. I have set up a directory exclusively for direct access styles which I use either from registrations or the Music Data Base. The next trick is to rename them with a numeric to keep the order, eg HeyJude becomes 1HayJude. Then I make this directory the default disk direct diectory and save it through system back-up. This means that every time I switch the board on it automatically goes to this directory.
2. The limited number of files per directory is a trap for young players (me to). I believe that it is a limitation of the operating system.
3. The screen flashing. (I have had my 9000PRO for about 8 months). This has happened to me on the rare odd occasion. At first I had a mild panic (I think I was in the middle of a number during a gig. I contacted my local Yamaha expert who did not know anything about it. He said that he would probably need the board for about three weeks to see what was wrong (!!!) I guess to be fair, the problem only occurs rarely, so it may have taken him that long to observe it. Anyway I decided that I could not be with out the board for that length of time, so I put up with it. When it does occur I find forcing a screen refresh (like pressing the exit or quick access keys) restores the screen to normal. I think if anyone can identify what the problem is so that a technician can quickly get in and fix it, then I will get mine fixed. The problem does not happen often enough to be of concern to me.

Jon.