For instance, if you lower the ending frame in the animation window, Poser will present a confirmation dialog asking:
"Are you sure you want to delete some of your frames?"
And you can select 'Cancel' or 'OK'.

Attached is a simple python script that does (almost) nothing. Try the above test, then run this script and try again. Then close the script and try again.

Any thoughts or ideas?

If I understand properly, I think I have seen this effect with P5 SR4, as well. I have some scripts which set up characters by loading figures and components and assembling them in Poser. Simple stuff, but some of them had problems. Files with certain names (Numerical names and names which closely resembled a folder name in a file path found elsewhere in the same script seemed to be the problems) simply would not open with Python. Python would apparently try to find them, then give up and move on. A script which encountered this problem, once it finished running, would print "The file was not found. Do you want to continue looking for files?" in the console window - twice. It seems to me that it must have been answering its own question and doing pretty much what you've outlined above. Or is that a separate issue?

Yup. That sounds like those confirmations were redirected to the console window.
I wonder if Poser hooks the Standard Error to those confirmation dialogs. Then when python starts up it gets redirected to the python console.

I wish I knew all the confirmation boxes that this can occur with. Deleting frames is a bad confirmation to miss. Something like 'Delete all files?' would be a real bummer.

I never noticed this with P5, but I'm not sure what service release I was up to.

thanks