Clean SSD install, random 5-6x boot increase shortly thereafter

I've been trying to reinstall Windows 7 Pro x64, but I'm having issues with boot time. Once the Windows animation appears, it normally takes ~5 seconds to get to a desktop (before the logo even forms), but within an hour or two, the boot time will seemingly randomly increase to 25-30 seconds. The few things I do before it happens are install the drivers Windows doesn't find, plug in my other drives, and run Windows update. Once the boot time increases, I've tried to system restore to a time before it happened, but only another clean reinstall will put the boot time back to normal. Usually, it'll be fine and I won't even change anything at all for many reboots, and randomly it'll start happening on the next one. I've also tried removing my other drives again, installing Windows as both UEFI/GPT and BIOS/MBR, and reverting practically everything I'd done except drivers and updates. Both SSDs I've tried are reported in good health. Clean boot still suffers from a long boot, and safe mode also seems to take long. Chkdsk and sfc /scannow both come back clean. I'm probably on around 30 clean installs and can't figure it out.

I made a boot trace, but I can't really interpret it, although it seems to be doing absolutely nothing with this extra time - https://www.dropbox.com/s/5cv9y9as7o...trace.zip?dl=0

Unfortunately Cluberti was our resident startup/shutdown trace goto and is not around these days but what your describing does not seem to far from the norm I would agree that is a bit of a difference from vanilla install to the delay but I would expect to see it go a bit after updates and drivers etc

Hopefully we have another member who can interpret the results you have

Sometimes drivers will "clash" for want of a better word at the moment . You could try a repair install. Heres a link to a tutorial on how to do that. Repair Install

You can also try these, just to make sure everything is o.k. : SSD - Install and Transfer the Operating System