I was in the same situation & bought a new printer, used up the carts that came with it & carried on with the compatibles - obviously, I bought the same model printer, as the compatibles' chips won't work across all models from one manufacturer.
If you've accepted any software/firmware updates from Epson since you've had it working with the compatible carts, that *might* be the cause - I've always thought it was what happened to mine.
Since installing mine, I've ignored the update messages - in fact, it's possible to disable them altogether. "Which?" put this out a couple of years ago, but it's inconclusive -
http://tinyurl.com/ycpy7tdo
I'm sorry that's not much immediate help, I hope someone can suggest something other than all the steps you've already tried.