I've seen a number of similar reports, but will post this one to help you solve this problem in version 4.
My system is Windows XP-Pro (SP2 + all updates) and based on the Intel P35/ICH9R chipset. The SATA drives are connected to the ports associated with that south bridge. The system is setup with the AHCI drivers from Intel. Like others, when you insert the drives they do not show up in the system's "Safely Remove Hardware" list. Likewise, they do not initially show up in the USB Safely Remove List either, however via the option menu you can force them to be listed.
Like others, I can only stop them via an "uninstall" through the Device Manager. When trying to stop them, USB Safely Remove gives the following message:
The error log entries are:
5/1/2008 9:46:30 AM ****************************** Start ******************************
5/1/2008 9:46:30 AM USBSafelyRemove Version 3.3.1.617 / Windows XP (5.1 Build 2600) Service Pack 2
5/1/2008 9:49:15 AM DeviceEject: VetType=VetoIllegalDeviceRequest, VetoName=IDE\DiskMaxtor_6L100M0__________________________BACE1G20\4&30374661&0&0.2.0
5/1/2008 9:49:42 AM DeviceEject: VetType=VetoIllegalDeviceRequest, VetoName=IDE\DiskMaxtor_6L100M0__________________________BACE1G20\4&30374661&0&0.2.0
5/1/2008 9:52:17 AM DeviceEject: VetType=VetoIllegalDeviceRequest, VetoName=IDE\DiskMaxtor_6L100M0__________________________BACE1G20\4&30374661&0&0.2.0
5/1/2008 10:25:57 AM DeviceEject: VetType=VetoIllegalDeviceRequest, VetoName=IDE\DiskMaxtor_6L100M0__________________________BACE1G20\4&30374661&0&0.2.0
5/1/2008 10:29:24 AM DeviceEject: VetType=VetoIllegalDeviceRequest, VetoName=IDE\DiskWDC_WD5000KS-00MNB0_____________________07.02E07\4&30374661&0&0.2.0
5/1/2008 10:29:37 AM DeviceEject: VetType=VetoIllegalDeviceRequest, VetoName=IDE\DiskWDC_WD5000KS-00MNB0_____________________07.02E07\4&30374661&0&0.2.0
5/1/2008 10:40:13 AM DeviceEject: VetType=VetoIllegalDeviceRequest, VetoName=IDE\DiskMaxtor_6L100M0__________________________BACE1G20\4&30374661&0&0.2.0
I very much want this utility to work with my system as going through the device manager isn't that convenient. Please let me know if your version 4 will solve this problem.