I'm not sure what is exactly going on in your case, but my experience has been that setting drives to spin down at all can be kind of a dicey proposition.
For systems on mains power (as opposed to laptops), the power savings are not very significant unless you have a very large number of drives that are both a) on 24/7 and b) idle for substantial periods of time. Modern NAS drives use about 3 to 4 watts when spinning and about half a watt when parked/spun down. If you left four drives spinning idle for a year, your incremental energy use (over parking them and having them draw .5 watt each for the year) would be about 30 kWhs, which (where I live) is about $3 per year of energy savings.
And if it were "free" from a performance and wear-and-tear perspective that might be worth doing ($3 is $3, right?), but spinning down at short intervals seems to hurt performance. And there's evidence that spinning down drives and parking the heads constantly causes more wear and tear on the drive than just spinning constantly (i.e. it's harder on bearings and motors to stop and start frequently than it is to just keep moving). For example many NAS drives are only rated to a certain number (500k or 600k) of "load cycles." Every time you park the head you're incrementing that "load cycle count." If it only goes up by a few a day, the drive will fail from normal wear and tear before you ever hit 500k, but if you're incrementing it 20 times an hour, 10 hours a day, you could wind up wearing out the drive a year or two early.
My advice is roll back the spin down to an hour or two hours, or just turn it off entirely (which is what I do).