The only role Alt-F takes regarding drive spin-down is to inform the disk drives to spin down after XX minutes of inactivity.
If the drives don't spin down is because they are being accessed regularly.
That access can be either from box running programs or from regular network access.
You can exercise that by logging into the box using ssh or telnet as the 'root' user, same pass as the webUI, and issuing the command 'hdparm -y /dev/sd?'. The drives should spin down and the bow two orange leds should shortly flash every two or three seconds. Issuing 'hdparm -C /dev/sd?' shows the drives current status (besides the two orange leds shortly (200ms) flashing).
After putting the drives in standby, you can logout, unplug the box network cable and , *without* using the webUI -- which in most of the cases have to spinup the drives to obtain its status -- see through the orange leds if the drives have been powered up. You can so know where the spinup comes from -- either internally by a running program, or through the network.
Some running programs might access the drives regularly, avoiding them to spindown.
Can you post the output of the command 'pstree'? Or though the webUI, System->Utilities->View Logs->Running Process
Have you installed any Alt-F or Entware package? The recommended way to install those is through a dedicated, always plugged-in, small USB pen drive with and ext3/4 filesystem; that way running programs from those packages will not powerup the disks.