When you have multiple files or at least one directory and recursive option selected, the Permissions box feature Leave as Is option in it's context menu, that effectively toggles all checkboxes to "undefined" (=leave as is) state.

I've documented this:
https://winscp.net/eng/docs/ui_properties#recursively

Often times I need to change the owner of an entire directory files recursively, but not the permissions. It would be nice to have a checkbox or something in the dialog that says something like "only change ownership" and then it grays out the octal permissions box. this would be for the RECURSIVE option, as this works as intended with a single directory with mixed permissions.