I noticed this when playing WinDEU's Sick Wubs course, which worked perfectly before, had this bug occur during the section at 3:18
It seems that the bug doesn't occur until a certain percentage is reached, and anything below that percentage makes the arrows invisible. The stealth mods at 0:45 in the course below work until a certain point.
If anyone needs information on the options i use, i'll provide them.
I'm running Stepmania 5 beta 3, on Mac 10.9.3, with the moonlight theme.