how does auto-optimized parameters works

In my recent analysis, I uploaded the same dataset twice into the program. The first run was conducted with auto-optimized parameters for LC-MS analysis, resulting in the detection of 5,128 features. However, when I repeated the process for the second time (two months later), the program only identified 1,851 features. I repeated the analyses multiple times in the second time receiving constantly the same result. I would appreciate it if you could explain to me about auto-optimized parameter and how that works.

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Note the details of the pipeline are described in this paper. The R code are at the GitHub.

We have studied extensively the parameters and related files, however we do not find out why this difference on the features detected occurs, as the data were exactly the same both times. We are wondering if an update occurred between our two analysis in the software that could result in this difference.
Additionally, since yesterday (21/12/2023) we get the troubleshooting page , both with our data and the 2 examples provided in the LCMS data processing. Would this be related to the recent update we saw it was released? We are hoping that this problem will be resolved soon!