Go back to 0.98.1, it's more reliable for many. Most people abandonded 0.99 as a lame duck.
98.1 beta seems to be the best in my book.. I run that on both of my 5 board Neptunes (or whatever we want to call them)
the newer cgminers are starting to have better features though, so hopefully we will be able to take those and run them on 98.1 beta (unless there are some new files in .99 that I needs that I am not aware of)
The file waas is new, i thing it does nearly the same what the old wasd does,
but i have no knowledge, which files handles this in fw 0.99.
We have to wait for the tuning suite, I think it will do this what happened with our RMA boards.
Reprogramm the eeproms on it.