hi, this was occurring with v2.1.1 in a multiplayer session with a headless server.

desync report
https://drive.google.com/file/d/1N3CL4vwcsGHDdPTHWvGxhplO1L180wmZ/view?usp=sharing

imgur link for icon reference clicked causing the issue.
https://imgur.com/XeccxjP

I'm not that familiar on how to solve a desync but I've added a per-client mod setting last version that might be the problem. Could you try a solution on your setup?

You just have to go to the WideChests_2.1.1.zip in both server and client and alter settings.lua. There is a setting with name "shortcut-tool" at the bottom, set "per_user" field to "false" on both server and client.

If this doesn't work I'll read up on desyncs and try to fix it.

it has removed the item from the menu selection, i do not know how to get the merge tool now to utilise this mod without that button :/.

This "shortcut-tool" setting toggles between merge tool available in shortcut bar and in blueprint library. Check mod settings and make sure "Chest merging tool only availavle as shortcut" is checked.

I tested it on an existing map and it still desynced.
Btw you can test it yourself by downloading the game from the homepage and execute it from there (Disable verify identity).
Since just picking up the tool causes the desync I would try to create a copy of the mod and remove everything (including even the actual chest merge logic) except for the raw tool and then add those pieces back one by one.
Because maybe its the actual tool/Factorio's hotbar logic that is flawed.

Ok, couple of minutes of figuring out how to start multiple instances of Factorio later: Desync is caused by shortcut callback modifying player cursor stack. Bilka looked over the code and said that should be a bug. So I'm reporting away.

In the meanwhile: workaround for this is to set "Chest merging tool only available as shortcut" mod setting to False on both server and clients. Merging tool will be available in blueprint library.

Bug fixed in Factorio 0.17.5