I don't understand what you say about formatting. I never make any complete format since you told me so. I only do a quickformat, as it's a must. In this case I tried with SFSformat that is a quick one too, and finally did a WB quickformat without filling any add.
I followed your fantastic "Quick Installation Guide for OS3.9 on WinUAE (with CD-Rom support)" at some points like create emergency disk and unprotect the df0, and I did with DH0 too, as it didn't write all when it tried to self-install os3.9 from the Sys4Aga I installed first.
Well, it's true that I coudn't make the OS3.9 start from the Emergency Disk, as it didn't find unit 0 (I tried with unit 1 and 2 too, although I only have one cdrom in the laptop), but I installed without it and OS telling I must do it from it, but (that's extrange) with the Emergency disk inside at the end it said as I was installing from the floppy, to press enter if it was inside, and I did so.
The thing is I could install BB1 and BB2, and it worked in the PC, but again it crashed in the Amiga. At least I know it has no relationship with Idefix, as it wasn't installed.
As I see it now, there must be some kind of problem with this Sandisk Ultra CF and the rom update, as I can't explain why the Transcend one works in the same Amiga doing the same.
I believe I will install it again with BB1, as I don't believe BB2 has to be so neccesary, or up to BB2 without rom update.