Renault have never ever been the same since the mass damper incident. The switch to Bridgestones also hurt them, but I thought they had recovered by the end of last year.
The car just looks like a handful. Alonso isn't helped with such a clutz as a team mate. Furthermore, I think the concerns over Renaults future, and budget cuts have distracted the team. They've moved away from windtunnel into more Computer based development, they think it'll work. If it does it'll take time. Maybe too long to attain the services of Mr Alonso 
You'd be surprised just how much niggly things such as you've said which are not directly related to the car etc. affect a team's performance. At McLaren from 2000 to 2006 all kinds of rumblings were happening off track, hence the team serially underperformed.

Ayrton Senna: WDC 1988,
1989, 1990, 1991
McLaren: WCC 1974, 1984, 1985, 1988, 1989, 1990, 1991, 1998,
1999, 2007McLaren: WDC 1974, 1976, 1984, 1985, 1986, 1988, 1989, 1990, 1991, 1998, 1999, 2008