Fortunately more and more organizations become aware that "managing by process" isn't about making nice process manuals, or implementing a workflow management system. More and more they start to realize it's about getting the right level of grip on your processes: Execute, Monitor and (when needed) improvement of processes.
Most organizations have more than one process and what I see so now and then is that, in the drive of executing and improve these processes, the "one size fits all" method is applied.
Think about trying to use a traditional workflow management system for a process that isn't suitable for this structured way of managing it. Or using Six Sigma techniques, where these statistical methods don't add much value to serving the (process) customer.
How is that possible, you think? For sure it is caused by the 'hypification" of some methods or technologies and solutions. Unfortunately that can lead to disappointment when it doesn't seem to work for your unique process.
You could call me old process fashioned, but I still think you need a proper understanding of what is going on in your processes and what you need to manage and improve them.
A straight through (oh, not in your organization?) like "paying invoice"; I'm pretty sure you can buy some kind of tool to do (or at least support) this.
But, a primary process that works with different types of customers, unstructured data and stubborn highly educated people; that's a different kind of process.
That's why I'd like to start with a process oriented view on an organization to determine the characteristics of these processes from there.
I'm pretty sure you will realize quickly that not all processes are the same and have the same demands.