I am experiencing the same thing since 1.7.0.
I’m sharing my Windows userprofile folder, which worked fine for many months. Since 1.7.0 I’m also getting exactly 13 Permission Denied errors on folders that cannot be normally seen in the Windows Explorer. That is, unless you enable “show system files” - then you can see the folders, but accessing them is not possible.
I fixed this by adding the problematic folders to the ignores. My best guess is that these are protected directory junctions/links (or similar) which are hidden to the user, but visible to applications. Syncthing previously ignored such junctions/links, but the new directory junction logic on 1.7.0 caused Syncthing to now attempt to walk these folders, which seems to not work.
For me the affected folders (see below) are all folders that seem to exist elsewhere, under different names, which assures my assumption that these items are some kind of filesystem hacks made by Windows.
The affected folders are (all relative to the userprofile folder)
Anwendungsdaten
AppData\Local\Anwendungsdaten
AppData\Local\Verlauf
Cookies
Documents
Druckumgebung
Eigene Dateien
Lokale Einstellungen
Netzwerkumgebung
Recent
SendTo
Startmenü
Vorlagen
Those folders are only visible when configuring the Explorer to show system files. They do not show when configuring the Explorer to show hidden files, which means these junctions have both the hidden & system file flag bit set. Accessing these junctions is apparently not possible - I’ve no idea why, or why they are there.
Anyway, to reiterate: Ignoring them fixed the issue and so far I haven’t seen any downsides.