Carefully follow that and it's possible
I haven't had a problem, already installed to 3 machines with the same disk. Technically, ML is below a single layer disk, but Apple made their image bigger.
That is very weird. It might have to do with the Apricorn Velocity card. Maybe you can contact them? Regardless, they can't do much.
Here is another thing you can do, but bear with me, it might take some time (and in theory it SHOULD work). If you have the time, give this a try:
1. Take out all drives from the system, even the Velocity PCIe card.
2. Put the 2 SSD's in bay 1 and 2 (might have to use a SATA+Power cable, or if you have the 2.5" to 3.5" converter, you're good to go. Or use the 2 Optical SATA ports (2009 MP and up), or the 2 ODD SATA ports (If you have a 2008 Mac Pro)
3. Boot off your USB and launch Disk Utility
4. Erase all partitions (to start from scratch)
5. Make a RAID 0 (splices for each), make sure it shows 240GB Total and format your RAID0 as HFS+ (Journaled)
6. Install ML from your USB drive (it will give you an error regarding Recovery mode and Filevault, ignore that)
7. After you're done, boot into OS X and see if all's working fine.
8. Turn off system.
9. Reconfigure both your drives to the way you had it with the Velo x2, ie, one on the PCIe board and one in the Optical bay via the extra SATAIII port on the Velo x2 (I wouldn't mount it just now, just leave it hanging to see if it works).
10. Start your machine to see if it boots into OS X, if it does, you're golden. If it doesn't, I would suggest that you just buy a bigger SSD (like a Samsung 830/840 Pro 256GB/512GB) and use the Velo as a SATAIII connector for the single drive and use all the other ports for mass storage (ie HDD's, etc). You can definitely resell your Intel drives or re-use it in the system as RAID 0 in the Bays for other stuff.
Hope this works out. It's a possible solution.