Nice spot Neemobeer, I was thinking along the same lines. Whenever I tried using GUI changing apps it also seemed to break something so I quickly learnt they best left well alone. We'll see I guess depending on the op posts..
Following a disasterous OS failure after doing a disc cleanup from which I could not recover, I re-installed the OS and am now proceeding to bring it up to date. The icons problem has gone away, at least for the moment.
Which leaves me with a truly massive update problem !!
I'd tried to make that machine replace this one by duplicating most of what's on this one, mainly by re-downloading applications where possible.
I didn't try disabling Kaspersky, but it might be worth asking them if they've encountered this problem before.
However, as I've re-installed the OS, unless and until the problem reappears, the cause will remain unknown.
I noted that although the batch file I used (above) is supposed to have rebuilt the icon cache (and did indeed bring back the real icons, at the end there was no IconCache.db file in /Local then or later.
As the icons were correctly displayed, I wonder from where the system actually obtained them - they must have been available somewhere else other than in IconCache.db !