When I re-open a saved scene with a cloth simulation Poser says it can't find (something), and I need to run the simulation again for each cloth.
Is this because I saved the pz3 outside the Runtime folder?

When you run a dynamic cloth simulation, it will leave a file called *.DYN (filename matches the name of your scene file).  This DYN file contains the morph data for your cloth simulation.  I've never saved any PZ3 files in my Runtime directory, so I doubt that's it.  If you rename the scene file outside of Poser, it may show the kind of thing you're seeing; from experience, if you re-save the file within Poser 7 after you have run a dynamic cloth sim, it won't error but you do need to re-run the simulation - Poser 6 didn't make you do this as I remember, I think it automatically copied the DYN files as you saved the scene file.

edit: small correction, filename for .DYN files is the name of your scene + the name of the cloth simulation, for as many cloth simulations are set up in your scene.

I'm using P6.
I've moved all the files in to the Runtime and reopened with the same problem.
It says it can't fine the prop that is clotherfied. Wish it would ask me to find it manually.
Poser said two props had the same name, this might be the problem. Poser said it needed to rename one of them.
Thanks for your advise.

Since we're on the subject here, a question just came up for me too....
(Poser 6) Isn't there a way to save different settings for clothroom, so they can be reapplied to different objects?  I'm in a mind blank!

I expect you can edit -> copy as you can with lots of other palettes, but I've never tried that.  You may want to look at Karanta's dynamic freebies here, as I believe they load with a lot of cloth room settings already done (written into the prop file).