I don't know about the failure to completely load, but I know what can make the splash screen appear off-center on your screen.
I guess you'll have to get the sim to lead before you can do this.
With the sim not in full screen mode (Windowed mode, I think is the proper term), "restore down" (as FS10 calls it) where the window doesn't fill the screen. Move the window to the center of the screen. The next time you load the sim, the splash screen will appear in the center of the screen.
If you end up needing to reinstall, first save your AddOn Scenery folder, your FS9,cfg and Scenery.cfg files, your no-CD FS9.exe file, , your main Scenery, Gauges, Effects, and any other folder you may have added anything non-stock to. In fact, just copy your whole FS9 installation to somewhere. Then do your new install and copy the developed items from the old one into the new one.
I had to do that when I moved to my current computer. I had complete copies of all my FS9 installations backed up on an external drive, so I just had to install FS9 om the new rig, make as many copies as I needed for my various installations, and copy stuff as required. It was a long and tedious task but not nearly so long or tedious as starting completely from scratch would've been. I got Golden Wings, FS1954, FSJetAge and FS2004 all rebuilt in a day.
Since you're having trouble with something unidentified, don't update everything all at once. Do one folder at a time and if the problem reappears you'll know where it's coming from.
And don't forget the files that FS9 puts into your Documents folder and [user]\AppData folders.
