Welcome @Janan_Gawra
Hopefully we can help! Would you like to capture a share link to the history with the problem so we can troubleshoot what may be going wrong? It is likely something small to adjust. You can unshare after. How to. → How to get faster help with your question
Or, you can try yourself? Inspect the input GFF data: are all data based on the same reference genome assembly? The identifiers are the same throughout? Are there any messages in the job logs? Mismatches are sometimes reported and give some clues.
We can help to troubleshoot the usage part first, then, if we can confirm a technical problem with a certain use case, we can get that reported and make suggested workarounds for the immediate term. My guess is that the data or parameters or tool version is slightly different between the two runs on different servers, since that is the usual case when comparing between runs, but we can confirm that too if you share two links, one for each server.
Let’s start there! 