This has been improved in 5.20.1:
https://winscp.net/eng/docs/history?a=5.20.1

OK, that seems to be the solution! Thanks for your help.

OK, I see what you mean now. The buttons are not reordered. It's just that when all of them do not fit, their viewing priority changes as you use them. That priority currently does not persist across WinSCP runs. What you can do, is that you can hide the buttons, that you do not use, to make sure that only the buttons, that you use, are visible. This is preserved across runs. Use Customize Toolbar submenu is the toolbars context menu:
https://winscp.net/eng/docs/ui_toolbars#customizing

OK, here's a screenshot. You can see the order of the commands is not the same as they appear on the toolbar.

I cannot reproduce this problem. Can you post few screenshots documenting the issue?

Yes, I already used that menu under preferences to reorder the commands. That did not change the order of the buttons as they appear on the Custom Commands Toolbar. The Custom Commands toolbar seems to have the buttons placed in an arbitrary order. When you make use of a specific custom command, that button moves to the front of the Custom Commands toolbar, but the order reverts back every time the application starts. I want to set the buttons on the Custom Commands Toolbar so that the most frequently used commands are at the beginning. It seems to that I was somehow able to do that previously.

You cannot reorder the buttons on any toolbar. It was never possible. You can only reorder whole toolbars.

You can order the custom commands in Preferences though:
https://winscp.net/eng/docs/ui_pref_commands

If you still believe that something has broken recently, please let us know.

Any suggestions on how to reorder the buttons on the custom commands toolbar?

I can't figure out how to reorder the Custom Command toolbar and make it stick. According to the documentation, I should be able to drag & drop items on the toolbar and then lock the toolbar. That's not working for me. It seems that the last option I use gets moved the front of the toolbar. Locking or unlocking doesn't seem to have any effect. I'm using v5.17.9 on Windows.

This problems seems to have appeared on a recent update. Before, the buttons were staying where I put them. Is there a solution for this?