Bit more information:

Opening a wooden crate still crashes the server. However if you open it in your inventory then you will be able to retrieve your things as normal without crashing the server. But as soon as anyone opens a crate that is on the ground or a player dropped one, then it will crash the server.

I have come to the conclusion [through some experimenting and trials] that the cause of the recent server crashes (the ones that happened this evening and were only down for a minute or so, but were frequent) are because someone somewhere is opening a wooden crate. The server happened to crash every time I open my wooden crate, exactly when I tried. I tried this two or three times to confirm and then realized it was me who was crashing the server (sorry about that ) But I am letting everyone know that wooden crates crash the server and should not be opened!