USB Hard drive problems after sleep/computer inactivity

Hi
I am the proud owner of a 2009 iMac after making the plunge and switching from my PC.
I am using my old Freecom 3.5" Classic 1TB external USB hard drive for extra storage and have reformatted one of the partitions to Mac OS extended (journaled) for use with time machine. i have left the other partitions in NTFS mode because I occasionally dual boot into windows. I have noticed that when I put the iMac to sleep and reactivate it or leave it unattended for a while the external drive powers down and cannot be recognised without switching it on off & on again. Sometimes the drive icons disappear from my desktop and other times they remain but without any icons inside the finder window when I open them. I also get the warning messages about not ejecting the drives properly and am worried I corrupt the data on them.
I have done a quick bit of research and have found that other people have described this problem with various brands of USB drives, however I can't find a definitive answer!
Does anyone have one? Your help would be much appreciated!
Thanks in advance!

I have the same exact problem... I know other people have the same issue; I've done research on the internet and we're not alone. Just no response from Apple or suggestions from anyone else. I find myself just mounting the disk as needed to eliminate the possibility of losing any data. I then use disk utility to remount when needed as opposed to shutting the drive down.

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