Quite often we handle situations when customer's IT department is installing Project Server 2010 internally using their general IT specialists. From time to time this leads to errors that hardly discovered but easy to fix.
One organization simply deleted farm admin from local admins group on servers in farm - it is unsecure from their point of view (disregarding that MS clearly states that this has to be done). As you can imagine you cannot make any change since you get access denied and other errors.
Another organization is not caring about configuring administrative backup daily schedule and resulting in loosing data because of change.
other organizations install Reporting services in DB server and insist that this is the way it has to be and it is our problem how to configure this.
Customers - if you install project server - PLEASE follow the guide from Microsoft and please do not change any configuration / setting after that. IF you have a chance - order an audit / assessment of configuration by one of the partners and follow their recommendations.