I have to admit I'm running into the same problem. During boot, right after "Executing startup scripts", the system starts generating the keys.
My setup is as follows (it worked on piCore 6):
I have the keys copied to a USB drive and I edit /opt/bootlocal.sh and create all the symlinks before starting the ssh daemon.
Now, to solve the issue, I have tried moving the symlink creation to bootsync.sh, thinking that it could help, but the keys were still being generated, regardless of the fact that the files were created before starting openssh.tcz (I removed openssh.tcz from onboot.lst to check if the keys were copied over to /usr/local/etc/ssh/, and they were)
As the last option, I used "filetool.sh -b" option, but the restoration process takes place after the extensions are loaded, so that doesn't help much, as the boot process is seriously slowed down.
I took a quick look at tce.installed script for openssh, but couldn't find any errors.
As a side note: I didn't use the openssh.tcz that is bundled with the RPi image. I manually installed it with tce-load -wi instead. Maybe the problem is there...