Please let us know the developer for this application you are using and if possible a screen shoot to verify the issue.
It is not a bug, it is feature. According to Intel "Desktop drivers don't include full support for hot swappable, the reason is because it was specifically designed for server board’s environment". You can find more details here: https://communities.intel.com/thread/48180
Although that should work correctly for eSATA ports, as long as you use proper driver. Don't use RST 12.8 it has a bug that does not register devices connected thru eSATA as removable, use either 12.5 or 12.9.
If your BIOS has an option to mark internal ports as "hot pluggable" and you are not going to use RAID configuration you can use default Windows AHCI driver, it worked for me in Windows 8.1, not sure about Windows 8 and 7. With Windows AHCI driver device will be correctly registered as removable if the port is configured as "hot pluggable". Hope this helps.