... When you add a second process diagram in a different area in the tree, if you reuse the pool then it starts to all go wrong...What are your thoughts?
The method that I use assumes there is one primary activity diagram that shows all of the possible flows. When the flows are too complex to contain in one diagram, I re-factor them into multiple child diagrams using Composite activities.
Doing it that way I believe would prevent the problem you are encountering, as the child diagram contains the child elements.
Let me know if that seems to work for you...
David
Side Note:
I use the UC's scenarios to describe each of the different flows through the activity diagram. Not all, but the ones that are sponge.. oops, I mean analysis worthy

I run code that extracts pathways, and creates a "scenario script" using the partition's name (e.g., User and System) and the text from the "notes" section of each activity or action encountered on that thread...
Example:
USER selects a report to be run.
SYSTEM prompts user to supply report parameters.
USER specifies and submits the report's parameters
SYSTEM validates the report parameters
SYSTEM etc...
One thing to be aware of... an action or activity is NOT associated with a partition in the database, but the upper right and lower left X/Y coordinates are specified for all elements that are "on" the diagram (actions/activities, partitions, etc.) so I run a quick function in the code to determine WHAT partition the element "belongs" to (accounting for elements that may touch more than one... ID the primary as the one that contains the "most.")