Thanks everybody.
I'm running Bitdefender and an early version of PrivateFirewall. MS Defender and it's firewall are supposedly disabled, but Defender still runs in the background, I've discovered.
After having some files/directories copied off another drive 'disappear' on pasting them to C:, I found they ended up in defender's quarantine.
I'm not particularly in favor of Bitdefender, but I had to replace Avira which had a growing false positive rate with every update, it actually quarantined a bunch of .h, .c, and .bat files several times on my win7 system - I discovered it's heuristics for removal sometimes depend on 'where' you keep a file, even if it's a text-based bat file (C:\users\owner was a no-no for non-system authored bat files).
On the win10 machine, I did try entirely removing Bitdefender before posting here to see if that would make a difference, but put it back on afterwards when the laggy first-run behavior persisted.
This acts like the system or something running on it are 'examining' files before allowing them to run or be moved on to the C: drive, I'm leaning towards MS Defender still being active, especially with the 'disappearing file' episodes.
On one occasion, I pasted a directory off another drive to C:, it pasted the folder and two of the files within the folder, but then took several *minutes* to finally paste the remaining files within the folder...extremely odd, sortof screams 'examination', eh?
Checking on the web, I do find instances of similar behavior on 10, but every case is different, often the OP's behavior descriptions are lacking detail and no general solutions popped up.
Thanks again for having a look, it seems we all suspect the same thing, generally, I'll post back if I have any luck running ti down.