I wasn't able to jailbreak, nor to root. But finally I got it!
Yes, there is indeed a limitation for the size of the bootable SD card! I didn't dive too much into it, but I guess it's the old 8GB partition limit.
The simple solution: I deleted the 16GB partition on my MicroSD, created a small 4GB one and left the rest empty. Now everything worked flawlessly: booting into recovery, jailbreak and root.
I guess I will buy a dedicated small SD card for hacking purposes.