Rate of pay: some of the jobs that exist at Applied do not have direct comparables at other organizations due to some unique structuring that exists at Applied. However, in many cases you will find that the market value for your work is more than Applied will pay you. Applied does pay an acceptable living wage, but the money does not beg you to give Applied your life-long career. Until this changes, Applied will be seen as a stepping stone by many rather than a career destination.
The CEO puts together presentations to the employees to provide updates on the progress of the company as a whole. This in itself is a good thing, but when coupled with the above issue, it is somewhat of a double-edged sword: I am happy to know that the company is doing great with record profits, but I am paid merely satisfactorily, and I can clearly see that profits support a raise for employees whose performance merits it.
Upper management is either unaware of or chooses to ignore major communication and role issues that exist between certain teams. Applied has multiple products originating from multiple original development companies, since acquired, and getting proper cooperation to happen between these teams can be somewhat challenging. It is not uncommon to get caught in the middle of a finger-pointing scenario, where an issue genuinely belongs to one team but that team has declined to own it, and another directly affected team has to fight to get the issue recognized and corrected.
Lower level management that engages directly with the employees tries to resolve the above issue, but it evidently does not get far enough up the ladder because long term resolution just doesn't seem to come.