Regular PS3 Ragnarok lets you program "on the fly" without connecting to the PC.
The USB PS3 Ragnarok doesn't have this feature. (It boils down to we ran out of room in the modchip's memory, so we couldn't fit both on-the-fly programming and USB programming into the same chip). It's also the reason why the USB PS3 Ragnarok has a few more features.
You could submit a ticket and ask the staff if you can send your regular unit in for a USB upgrade, I think they could do it cheaper than buying a new unit. Unless your controller is already worn out then it might be worth buying a new one but if you ask the staff for a repeat customer discount they can look up your old order and get you a repeate discount.