SAMtools does not produce a complete list of variable positions

Сomplaint from the company Vector-BEST:

When analyzing NGS data, we sometimes need a very deep search for variable positions (options with very low representation). To do this, we use the Samtools built into UGENE.

The first time the problem arose at the turn of 2016-2017: i.e. in the 2016 versions we got another large set of options in the vcf file, and in February 2017 we got a very small one from the same data set. Moreover, if you look at the sam-file in the UGENE Assembly Browser, you can see that there are really a lot of options.
We were advised to replace the latest version in UGENE external tool Samtools folder with an older working one. Since then, for 5 years, every time after installing a new version, this replacement has to be made.
Scenario:

1. Load in Workflow Designer attached SAMtoBAM+sort+VarCall_0222.uwl
2. Select "Чтение последовательности 2" item and add "hbv+AdV.fasta"
3. Select  "Получение списка файлов 1" item and add "sS1-3.sam". Extract this file from "ftp://ugene-quad-ubuntu/test/UGENE-7587/sS1-3.rar.
4. Run workflow and save vcf file as vcf_2022
5. Replace external tool SAMtools with tool attached SamTools2016
6. Run workflow and save vcf file as vcf_2016
7. Compare vcf files