not sure if this is your problem but i think most shells (like bash) don't add the history in their buffer to the common history until you close the session. th

not sure if this is your problem but i think most shells (like bash) don't add the history in their buffer to the common history until you close the session. thus recent history in one window is different than another. That _may_ be what you're dealing with. I believe there are ways to tweak it to always write everything to the common history immediately.