It is always nice to see experienced people whose requests are not that easy to resolve (unless you work in the support team of a software vendor).

Even though it is a good idea to uninstall the previous version before installing a new one, I have both WMR 11.3 and WMR 12 and both work perfectly.

However I suggest you to uninstall both versions and install only one of them.

When switching to the PRO mode do you see the following message: "PRO mode successfully setup"?

Also go to Settings->Media options tab and make sure that Windows Media in the Captured File Types group is checked.

p.s. Actually I don't see any big reason to upgrade. WMR 12 can now change to ADA mode much faster so sometimes I don't need to close all the applications that use my internet bandwidth heavily. However there are some features that you need like improved reprocessing and scheduling... Of course you might just like WM Converter....