i get those little red x's on the operation screen in emplode

Against which items? Sometimes if the player's taking too long to rebuild its database without reporting progress, emplode will give up on it and fail out the rest of the steps. It still finishes eventually.

Basically, if the player isn't rebuilding the database every time you turn it on immediately after the sync, then it all completed OK, and the only thing that didn't work is emplode refreshing from the new database on the player.