Differences in results between versions 1.2.0 and 1.6.0

[Niveda-S]

Hi,

I was trying to use the same dataset across two different versions of probatch 1.2.0 and 1.6.0. There sees to be a huge difference in the results between the two versions.
I. For example, for the same dataset, the PVCA using version 1.2.0 shows batch corrections but using 1.6.0 shows no batch correction:
a) Version 1.2.0
Before Correction:

After Correction (Combat+Loess):

b) Version 1.6.0
Before Correction:

After Correction (Combat+Loess):

II. Similarly, the PCAs looks super different:
a) Version 1.2.0
Before Correction:

After Correction (Combat+Loess):

b) Version 1.6.0
Before Correction:

After Correction (Combat+Loess):

This is only for combat+loess results. Running just combat produces identical results. What is the reason for the difference? It looks like version 1.6.0 does not do batch correction at all. Should I be using version 1.2.0?