Hi,
Please, always send complete code. I cannot reproduce your results if I don't know what are the objects you use, or which packages you have loaded.
Also, I don't know what you mean by version 1.4.1 of xAct. The most recent version is 1.2.0. Do you mean a version of xTras, perhaps?
I'm not immediately surprised that you get different results when metric-differentiating expressions with different metric factors inside. I'd say you always have to use tensors with the proper index-character (up or down) when computing variational derivatives. Otherwise you rely on more-or-less arbitrary decisions of whether internal functions use or not ContractMetric and SeparateMetric internally, that remove or add metric factors. Loading some packages (other than xTensor) can change some of the default settings in this regard, for example.
Cheers,
Jose.