As you pointed out, in the latest beta we have modified how library works: if a style which is used in the scene is loaded, this is re-applied to all objects with same style.
A problem with that, is how to handle the Parameters: it's possible that you want to update some of them, but keep values for others. Initially, there is no way that plugin know thats.
To solve this issue, we detect what parameters has been modified for the user, and these are not overwritten. But this mechanism works only if the object is edited with the beta (o a later release).
For this reason, now most of your parameters are reset. Once you work with the new version and edit these objects, this problem should not happen.
Regarding materials, RailClone should not create duplicate them. If a material already exists in the scene, the library just uses or replaces it, depending of the option selected here:
Futhermore, the plugin doesn't create XRef materials. These always are imported normally.
Are you using a standard or custom library ? What option is selected for duplicates ?