theWord

I am accustomed to The Word retaining settings when closing, such that when it reopens they are in the last-used state. For at least some of them, this is no longer happening. I have mainly noticed this in regard to the "Detailed" tab in the Bible Search window. It now keeps defaulting to "Whole Words," even though that is not usually what I use or desire.

This behavior seems to coincide with the installation of BDAG, which has a possibly similar issue: Every time I start The Word, it informs me it has just noticed that BDAG has been installed, and gives that little dialog that asks whether I want it included among the displayed items. It repeats this every time, rather than remembering from the previous session.

Are there any other recent programs you have installed? It is almost certain that the config.ini file that contains such settings is not being written to. Again the same with the BDAG. So is it possible that Anti-virus is blocking things?

As Jon said, this is because the folder that theWord is writing the config.ini is not writeable.
I cannot tell why this happened to be honest.
You can either fix the permissions on that folder (this should be the 'Personal' folder) or just re-intall theWord and let the installer deal with it,
Costas