The Unofficial Daedalus does not flicker in-game, but has depth problems and missing movies etc. ahe Unofficial RSP solves some of the sound issues (don't overwrite your original with it though) I find the game the most playable in this way. Use PJ64 1.5 SP1 as this game is pretty unstable.
The only viable alternative is Jabo's D3D6 1.5.1 (still using the Unofficial RSP). Like the Unofficial Daedalus, it also has major problems both in-game and out of game. If that don't work, then you won't have much luck, as this game has most of the movies missing which makes it look like it has frozen, depth problems, missing audio etc.