Your best option for a thorough boot-time scan is to get a pre-Windows scanner. With this kind of scanner, you create a bootable disk with the scanning software on it, and you then boot with that disk. When you do it this way, Windows never loads, and so the a/v software can do a much more thorough scan of your hard drive / computer.
The most well-known of these pre-Windows scanners is Windows Defender Offline (WDO). This program is free. You can get it at the following web site:
https://support.microsoft.com/en-us/...-protect-my-pc
Scroll to the bottom of the page to get the Windows 7 / 8.1 version of the software. Make sure you select the correct version of the program that matches your installed version of Windows (32-bit vs 64-bit).
I don't think WDO is the best software out there. But it is good enough to find whatever has buried itself so deeply into Windows that you can't clean your hard drive with normal a/v software.
WDO takes a while to run, so be patient.
Trend Micro has a similar program. You'll need to install Trend Micro onto a computer in order to be able to create their pre-Windows scanner. You could probably go with the Trend Micro free trial version. Trend Micro is one of the best a/v programs on the market, so I recommend going with than one rather than with WDO.