I've noticed this for some time. Nadal made a big fuss last year in Dubai when he played Youzhny & Hawkeye didn't agree with a clear mark on the court.
The creator of Hawkeye had an interesting explanation, saying since hawkeye sees the ball better than linesman, etc, even a mark on a court isn't necessarily an accurate reflection of where the ball actually hits.
So in essence, he's saying marks being used to uphold or overrule calls during claycourt matches may not be accurate.
Let's be honest, the main reason hawkeye is being used in tennis is not to help the players, get it right, etc, but mainly to increase fan interest. The ATP wants tennis to be more about entertainment than sport, & this is part of a concentrated effort to make it happen. If they knew the system was flawed, they'd probably turn an eye to it(heck, they turned a blind eye to gambling issues until last summer, even though they knew how serious it was for many years)