Ahh, I didn't realise that more than one app can share a UID. I had thought that all the Sony apps are different UIDs, but if I look closely I can see for example that reader and netapp both use user ID 10006.
I've set my reader shared prefs file to mode 664, and then changed the default font size and that at least didn't reset the permissions. I'll see if it sticks or gets reset at some stage.
The sledgehammer would be for your app to run as root but that does seem like overkill.
Off topic - there's a pref in the xml called SpreadDirection, set to 0. Does that make any sense to anyone?