Over the weekend, I did a reinstall of OS3.9 to my A1200.  I repartitioned the disk, formatted it and installed OS3.9.  I then applied BoingBag 1 without an issue and then applied BoingBag 2.  I did not receive any errors during the install, but I did when I rebooted.  I received a recoverable system error 0100-0003 which means an exec library check sum error, IIRC.  The system continued to boot and once it was up, I did some checking around of versions...
  Kickstart was 40.68
  Workbench 45.3
  exec.library 40.10
  ROMUpdate 44.26
  console.device 44.6
  shell 40.2

I checked on my A2000 (which also has BoingBag 2) and I saw the following:
  Kickstart 45.57
  Workbench 45.3
  exec.library 45.20
  ROMUpdate 44.57
  console.device 44.8
  shell 45.7

When prompted whether to install the ROM Update or not, I selected yes to install, but it seems to not have worked.  I then copied over the "AmigaOS ROM Update.BB39-2" copy and rebooted with the same issue.  I then powered down the machined and waited for well over five minutes and tried again with no success.  Do I need to do anything else to get the BB2 ROM Update?  Has anyone else seen this behavior when installing BB2?  Note that the BB2 came from the same source as the one applied to my A2000.

Thansk!

is your a1200 expanded ?  ie a turbocard ?

I have a daughter board with 4 MB RAM and RTC combo and I have a Compact Flash PCMCIA card.  Those are the only expansions.

It sort of happens after both cold and warm boots...

Perhaps this is a related issue, but I'm not sure.  I'm using a Compact Flash device as an IDE drive and when I perform a cold boot, it says that it cannot find a boot device (you see the rainbow check mark and the floppy being inserted into the drive animation).  If I place a bootable floppy in the drive, it starts to boot and then at some point during the startup-sequence, it automatically performs a warm boot.  At this point, I remove the floppy and it boots normally from the CF device.  But, this was a problem with both OS 3.9 and OS 3.9 w/BB1.  The CF2IDE card is missing the jumper to switch from the device being Master or Slave and it defaults to Slave.  I'm planning on installing a jumper and see if that clears up the problem as I don't see this with a traditional IDE drive.

No, it does not.  I also thought it might be a timing issue with the CF2IDE card but I let it sit for a good minute or so and attempted a warm reboot with no success.

Yes, I can put the drive in that I just took out.  It's a 256MB Seagate with either OS 3.1 or OS 3.5 (I don't recall).  It was booting just fine when I last used it.  When I open the 1200 back up to put a jumper on the CF2IDE card I'll first put the old IDE drive in and see what happens.

Well, I'm not too sure how similar they are now that I've found a fix for mine.

Basically, I did as Craven1200 asked and swapped out the CF/CF2IDE and replaced it with the original IDE drive and it booted up just fine.

So, I took the CF2IDE and added a jumper block and jumper so that it is now set to the default IDE device on the chain instead of the slave.  The cold boot no longer required a floppy, I did not see the recoverable system error and the library/ROM versions were as I expected.  I then did a warm reboot and had complete success as well.

So, I guess the lesson here is not to attempt to install BB2 or cold boot from an IDE slave drive!

Thanks for the help!