When you look at config options there's a drop down menu listing each source of information that ends up in the current config. When you select each of the files it shows what contribution that config made.
Typically PTC looks in order, in the installed directory, then the start directory for the app and then the Users home directory, picking up details from each in a cumulative way. You can also manually load configurations from any locations and they can be .txt suffixed files, as long as the contents are text. This last is what I have typically done - the main config.pro contains only a mapkey that loads the rest of the config from a text file.
You can change where the start directory is for an application under the properties for the shortcut for that application.
I wonder if your reinstall put in a graphcs driver that is not compatible. There have been cases where users had to go backward for a compatible driver or get a driver from the computer manufacturer, not the graphics chip maker. It may take a few tries as there is no good guide for this beyond the supported list from PTC; I'm guessing that
GeForce cards have been discussed over a long period of time for use with ProE/Creo, but they are not a favorite. I don't know if you can reconfigure to use a card from the Quadro line, but that's been the go-to GPU line for a long time. Here's a long thread on the subject http://communities.ptc.com/thread/54591
