Hijacking this thread a bit....my problem does not entirely match.
I decided my PAL A1200 (stock '020, zero FAST RAM) will become a dedicated game machine. I have a spare 16GB SanDisk CF card available since I upgraded another machine to a larger card.
Since the A1200 will be modestly spec'd, I will keeping the OS to v3.1. I will be throwing everything on it WHDLoad-wise, including demos so I most of the space will be used but will still have a lot of breathing room.
I prepped the card using WinUAE as I have done successfully in the past. I used the PFS3 handler for the file system and did the scsi.device patch to cover the large drive size. My partitions are: dh0 2gb, dh1 6gb and dh2 8gb. Everything went smoothly and I even tested the system successfully by matching the specs of the stock A1200. I ended up with ~700k chip ram and 0 fast ram with the ClassicWB lite install. Of course, not much in WHDLoad will work with zero fast RAM and I expected that. I plan to pick up a cheapy RAM expansion soon.
When all was done, I popped the CF card in the A1200 and fired it up. The system booted but then I was greeted with an insert volume "Work" message. Ehh? The system booted fine from the dh0, but my other two partitions are not recognized! They show up as non-dos on the Workbench. I loaded up HDTools and can clearly see the other two partitions and their correct partition sizes but they are not mounting.
I returned the cf card to WinUAE and all is well again.
So, how do the two systems differ? Well, I have Kickstart 3.0 ROMs in the real A1200 but I do not think that matters with PFS3. The compact flash adapter might be questionable though. It is one of those all-in-one right-angle units that just sits on top of the IDE header (no ribbon cable). I became aware that some CF cards are not recognizable with this adapter on a cold boot. If a soft-reset is done, the system boots fine. This is not quite what I am seeing though. It boots from DH0 on a cold start OK but not mounting all partitions. If the adapter were to blame, I do not think it would boot dh0.
I suppose I could pull the CF adapter from my other A1200 (that one uses a cable) but I really don't want to pull that system apart right now.

Is there something else to blame here or should I hunt down a better adapter?