I did some searching and found a couple of threads in regards to this issue, but none brought up using DISKPART to fix the issue. I recently bought one myself, and found that some SD/microSD cards doesn't seem to boot even after using FDISK to clear everything out.

I thought it had to do with some SD cards were made, but I found the DISPART/CLEAN trick that made every card I had boot!

Before using the SD Card in the adapter/retro PC, mount it on a modern Windows machine. The command we're interested in using is DISKPART, so I believe the earliest Windows that may have it may be 2000 or XP, but definately Vista and up has it.

BE CAREFUL YOU HAVE THE RIGHT DISK OR YOU WILL DELETE EVERYTHING ON THE WRONG DRIVE! Should be easy if the SD Card is the smallest drive in the system.

Open up the command line (cmd.exe) as an administrator. Type "DISKPART" and hit enter.

Then follow the example below. In my example, Disk 2 is my SD Card (2 GB card).

DISKPART> list disk

Disk ### Status Size Free Dyn Gpt
-------- ------------- ------- ------- --- ---
Disk 0 Online 894 GB 1024 KB *
Disk 1 Online 2794 GB 0 B *
Disk 2 Online 1886 MB 0 B

DISKPART> select disk 2

Disk 2 is now the selected disk.

DISKPART> clean

DiskPart succeeded in cleaning the disk.

DISKPART> exit

Leaving DiskPart...

In the example above, these are the commands you type:
DISKPART
list disk
select disk 2 <---- Make sure you are selecting the right disk!!!!!
clean
exit

Take the SD Card out, put it in your SD to IDE adapter of your retro PC. Boot up your DOS or Windows 98 install disk and use FDISK and FORMAT like you normally would.

I hope this helps someone out! It saved me a lot of trial and error trying to test which cards allowed booting and which ones doesn't. It turns out they all did, as long as you "clean" them.