On most of the Arduino Mega 2560 boards (clones can vary) they have a chip that talks to the USB (usually in the corner near the socket). This chip is actually a tiny Arduino in itself, so it's programmable.
My guess is that the programming on one of the chips (they're usually ATMega 8u2's) differs to that of the other, which is why the older one doesn't work with the newer drivers.
Easiest/fastest way is to buy two new Arduino's from the same place. They're most likely to have the same code on the 8u2's. This isn't always a cheap option (depends on how you value your time and how cheap you get them, shipping, etc).
The other way is to get access to an ICSP for Arduino (such as the Adafruit USBTinyISP) and reprogram the 8u2's on the boards with the same version of code. If you've got a hackerspace nearby, they may have one if you don't or can't afford one. If they do have one, Hopefully someone there can help you through the process, as it's not a really simple thing to do. It's not too hard, but can be daunting if you've not done it before.
If those boards are in any way different regarding how the 8u2's are hooked up, you haven't got a hope. That is fairly unlikely though, as almost all the clones are just that - clones - direct copies of the boards. They don't change anything as then it's more work for them (eg: getting code written that works with the new arrangement).
I would visually inspect the boards. If they look identical, then you should be able to reprogram them. If not, I'd look at either getting two identical new boards, or taking a chance that you can buy one that matches one of the two boards you already have.
Hope this helps.
My guess is that the programming on one of the chips (they're usually ATMega 8u2's) differs to that of the other, which is why the older one doesn't work with the newer drivers.
Easiest/fastest way is to buy two new Arduino's from the same place. They're most likely to have the same code on the 8u2's. This isn't always a cheap option (depends on how you value your time and how cheap you get them, shipping, etc).
The other way is to get access to an ICSP for Arduino (such as the Adafruit USBTinyISP) and reprogram the 8u2's on the boards with the same version of code. If you've got a hackerspace nearby, they may have one if you don't or can't afford one. If they do have one, Hopefully someone there can help you through the process, as it's not a really simple thing to do. It's not too hard, but can be daunting if you've not done it before.
If those boards are in any way different regarding how the 8u2's are hooked up, you haven't got a hope. That is fairly unlikely though, as almost all the clones are just that - clones - direct copies of the boards. They don't change anything as then it's more work for them (eg: getting code written that works with the new arrangement).
I would visually inspect the boards. If they look identical, then you should be able to reprogram them. If not, I'd look at either getting two identical new boards, or taking a chance that you can buy one that matches one of the two boards you already have.
Hope this helps.