Hmmm.  It seems my problem was I had the old files from June 2018 still in the config folder as well as my current one in the DATA directory.  It had been working fine but until the latest Rust update but it seems like now it was pulling my stack sizes from the old file.   I deleted it and now Stack sizes are working fine again.  /shrug

So everytime I restart the server, the stack sizes go back to defaults.... but if I unload and then reload the plugin, then it's working again.   Not sure why...

You can leverage the new system where the config informs the data file for new items for migrating to the new way of doing things. Unload plugin. Delete data file. Set values in config such as resources.25000. reload plugin. Data file will generate and all resource item types will be 25k :)