@supersaiyancurry thanks.
I have a part of the explanation. You can't see your roms, configuration, etc. because Recalbox can't access your share partition on this SD card. So in this case it mounts a virtual share partition in RAM, with default values.
Filesystem Size Used Available Use% Mounted on
/dev/root 1.9G 903.2M 905.2M 50% /
devtmpfs 236.7M 0 236.7M 0% /dev
tmpfs 240.9M 0 240.9M 0% /dev/shm
tmpfs 240.9M 120.0K 240.8M 0% /tmp
tmpfs 240.9M 2.8M 238.1M 1% /var
tmpfs 240.9M 104.0K 240.8M 0% /run
/dev/mmcblk0p1 63.0M 7.0M 56.0M 11% /boot
tmpfs 128.0M 100.5M 27.5M 79% /recalbox/share
During the boot process, we can see errors:
[ 2.977520] EXT4-fs (mmcblk0p3): couldn't mount as ext3 due to feature incompatibilities
[ 2.986321] EXT4-fs (mmcblk0p3): couldn't mount as ext2 due to feature incompatibilities
[ 2.996573] EXT4-fs (mmcblk0p3): bad geometry: block count 7306306 exceeds size of device (7046210 blocks)
So according to me, @Substring is right, even if the 2 cards seem to be the same, they are not identical, and the second one is a bit smaller. There is nothing you can do easily under Windows...