Nepotism - When a job is opened, it is clear who will get it before the process even starts - the hiring manager's favorite. Interviewing for positions is basically a waste of time unless you've been "tapped" and only serves to tick HR boxes. The same goes for promotions - the most deserving rarely get them...
Insecurity - constant re-orgs by the parent company leave you feeling one re-org away from being out of job. Good people are jumping ship for a little security as it appears most headcount is now heading overseas..at least in IT
Salaries: not keeping up with Bay Area reality. Management keep saying they are addressing it..but they are not. It's almost as if they don't want to attract the top talent anymore. People jump to other companies to get their fair market value - particularly in the Bay Area.