This is total guesswork... but:


It's entirely possible that NEStopia may not be reloading the states from disk when you load state.  It may keep the last few savestates saved in memory for other purposes (rewind functionality comes to mind) and simply uses that copy since it's already loaded, rather than having to reload the state from disk.  The fact that you need to reload the ROM supports this hypothesis, since NEStopia would clear all its movie/rewind and state data when loading a new ROM -- which is something it wouldn't have to (or necessarily want to) do on a simple soft reset.

If that's the case, you're screwed.  Short of making a custom build of the emu to ensure it reloads the state from disk every time, I don't know how you'd get around it (unless there's a option for it in the menus somewhere?)

Try disabling rewinding ability, movies, and anything else related in the emu to see if that does anything.