Yes, when a battery is running low the board will reboot and can get into a loop of booting up, startup sound plays, power drops, reboots. I do mention this in the instructions ;-)
PP3 9V batteries are great, nice and small and light, but they don't have much staying power, that's why I do recommend using 12v with 8 x AA's ideally for much, much longer run times.
You'll also get a bit more volume from the amp with 12v compared to 9v.
Not sure Shea why you're getting a problem with hovi speakers. Could be their rating, ohm/watt, or could be how they're wired, serial vs parallel, or some other wiring issue. Would need to see the setup (photos) to make a further diagnosis.
Worth noting too that batteries don't like the cold and this will drastically reduce their performance. Also cheaper brand batteries or dollar/pound store batteries are fine for TV remotes or simple toys, but high drain devices such as digital cameras or my ROM/FX need heavy duty batteries. I recommend the Duracell Ultra or similar like the Energizer Ultimate.
Thanks,
John