Hi, I just bought a new LS-QVL (Enclosure) and faced the same problem of unable to format a 2nd HDD. After much fidling around I found that following will help solve the problem.
1) Remove all HDD in the LS (Inlcuding your 1st HDD)
2) Put your LS into EM mode
(Hold Function Button while pressing On button. You should see that the both Power and Function button will start blinking. Press Fuction button again. Wait for awhile and you should see that all the HDD activities light turn red and NasNavigator show that LS is in EM mode)
3) Power off the LS and insert only the 2nd HDD (Dont put in the 1st HDD) into the 2nd slot
4) Power up the LS and enter to EM mode again using the procedure in step 2
5) Download the Firmware updater for yoru LS and update your LS. You may need to edit the LSUpdater.ini (using a text editer) to change the line "NoFormatting = 1" to? "NoFormatting = 0"? to force an format of your 2nd HDD.
6) Wait for awhile for the Firmware updater to format and initialise you 2nd HDD.
7) After firmware update completes, power off the LS and re-install your 1st HDD. a
8) Enjoy!
Hope that works..... it works for me at least.
Cheers!