do the usual 'startup' dance:
1) comment out your user-startup in your startup-sequence using a semi-colon, so it is ignored on bootup;
2) drag anything in WBStartup out of there so it's not started either
3) since you're using 3.9, you need not employ much of the hacks people use on earlier OS versions BUT, some of them still don't work on 3.9 so you might wanna stop using them anyway. .
Then reboot and see if you get things working again.
Also, try making sure your CD-rom support is correct and not messed up - I noticed in a brief experiment with 3.9 (had to go back to 3.1 due to incompatibility with some of the programs I wanted to use, unfortunately, really didn't want to) that it copies a 'secret' emergency CD-rom driver into the Devs dir and that seemed to prevent a correct bootup in some cases.
Does the computer boot correctly with your'emergency startup' floppy? Because if so, check startup parameters there vs. your regular setup and see what's different, and change as needed.
The point on Picasso96 is a good one - I couldn't get my C64/3D to even work on my A2000 (even though it was brand new) until I gave up on CGX4 and went to Picasso96 - worked first time!

But that didn't help my other computer, an A3000D with a CybervisionPPC graphics card - Picasso96 doesn't support that one, doh!
Good luck!
kevin orme
amiga university
www.amigau.com