Keeping the disk spinning all the time is a big power drainer.
It was all working fine with the iPod interface but when I put the current build of Rockbox on to it, the hd will spin down after a period of time and will not come back up even if rockbox is trying to access it.
I admit I don't know too much about it, but from this description it sounds like it could have to do with the fact that Rockbox powers the hard disk off completely a short while after it has spun down to save power. I would
guess that this doesn't work with every hard drive. On the 4th generation (and newer) Ipods Rockbox does that since revision 15444, so maybe you could try an earlier one - you would need to compile your own or find someone who compiles one for you.
You might want to also join in IRC (see link in the left side menu), maybe there are people around who know more.