I've had zero issues every time I flash mine and the carts I've tested on my PC flashed without issues as well.
As for the driver discs, I only checked to see if the packages contained discs, I did not open, handle, masterbate with, or otherwise fondle them in any way, shape, or form. They are practically useless anyway since better software can be downloaded from the neoteam site.
Compatibility wise, I've only had problems with 5 US titles not wanting to start, freezing at the menu. That is even after ensuring the header is removed. I've only tested/played the games on my unmodded TE, so I suppose compatibility could possibly change depending on the system.
Here is an interesting development... That "bad" cart I swapped for neoxeno appears to be very much functional and works very well... just on certain systems. It failed to operate on my Express as well as my TG16, but operated flawlessly on my Supergrafx, Duo-R, and modded Core. I'm beginning to wonder if people aren't pointing the finger in the wrong direction.
Perhaps the carts innards might be different from the rest, requiring more juice to operate than the others. Any thoughts?