Not super reproducible, but generally seems to be caused when I switch windows and then switch back to Minecraft and the cursor is gone. Happens rather frequently (enough to be quite disruptive to my work).
Was introduced around the time of the LWJGL update, the cursor is still there and can be used to select menu buttons etc, but it is invisible which makes this difficult.
Confirmed on Debian with KDE. Tabbing out while in-game (with auto-pause enabled) seems to reproduce this consistently; unpausing and pausing the game fixes it.