Hi,
No... The Boot Drive is supposed to be the main OS partition, The System Partition is where the built in Windows Repair files are stored...
But you have another one at the end of the drive as well...
It most certainly wouldn't hurt to make the 549MB partition active, and make the main one not Active and see what happens...
It is possible the "Repair" placed the repaired boot files on the flash drive as well...
It is strange that the front USB Ports only work with the installation flash drive... Is it a USB 2.0 or 3.0 Port ? There is a Bios setting for the USB 3.0 Support also..
It is possible that the HDD has files that the SSD is looking for, and is getting them from the flash drive instead... I'm thinking\hoping they are someplace other than the OS partition...
That is why I suggest to hide and make Not Active the OS partition on the HDD for now...
If it still won't boot properly without the flash drive, Unhide the HDD OS partition, but leave it Not Active...
Another thing you could try to get the flash drive out of the picture might be to put your installation media on a DVD, and force the repair to put the files on the SSD...
You could try hooking everything back up like it originally was...
Just make the SSD OS Partition Active, and the HDD Not Active, and try again...
Might be best to try a DVD for that also... Less confusion for the Repair functions...