1. Cost focus. In a cost-focused organization (as opposed to revenue-focused), such as universities and certain enterprises (mostly, IMNSHO, large SaaS enterprises), much of the development is performed by lowest-cost developers, meaning those without UX experience or training.
2. Training. Project managers don't know better. In order for the PM "customer" to evaluate good UX, (s)he must know what good UX is. Without some exposure to heuristics to evaluate a good US, it won't ever be a consideration in planning or accepting the project.
3. The larger the organization, the more likely the PM "customer" is not an actual user of the product. Corollary: the larger the organization, the greater the likely distance between the developers and the customers.
4. Inertia. Some large companies still use terminal systems or require IE6. It's more difficult to change than it should be.
5. User lock-in; lack of substitutions. In environments where users don't get to choose which system to use (e.g., students using a university's learning management or registration system) and can't turn to substitutes, the incidence of poor UX seems higher. These are also situations where users have little bargaining power relative to the developers.