The problem is that WinSCP simply refuses to open some local directories (yes, local!) Double-clicking the directory does nothing, right-clicking HIDES the directory from the panel (although right-clicking on another directory or refreshing makes it reappear), and if I try to drag content from the "forbidden" directory (opened in Windows Explorer) to the remote pane I get an error saying "System Error. Code: 3. The system cannot find the path specified".
In reality the path is very much available, and there are no special permission issues that I'm aware of (I open those directories in Windows Explorer in the usual way, with no acrobatics whatsoever); the files therein are also quite bland, there's absolutely nothing special about them (they aren't huge, there aren't a lot of them, there's just nothing special about those directories).