I still had the log window open when I turned on my PC this morning and I noticed (in your CSV log header) that your FOL set at 90. Was this done on purpose or by recommendation by someone? Typically FOL is set between 50-70 for GTI's and Golfs's here in North America, but it does depend on other mods/settings etc. For a typical JB4 setup, Golf 1.8's are usually set on the higher end (60-70) and GTI's on the lower end (50-60). If it is set too high, the higher fuel pressure the JB4 requests can cause the fuel pump(s) to not keep up with demand.
I think your best bet is to work with George @BMS to help troubleshoot this particular 1.8t variant used in your Skoda. Many ROW 1.8t variants are different from the North American 1.8t Golf and will behave differently when tuning with the JB4. For example, many ROW 1.8t's have variable exhaust valve timing while the North American 1.8t does not.