Almost certainly has to be something else going on there Lonk. I know that Ruud specifically fixed this in 4.52 as I was one of the ones that complained it wasn't working right in prior versions.
Release notes for KiXtart 2010 (version 4.52)
New functionality/enhancements:
1) CompareFileTimes has been enhanced so it can operate on open files.
2) RD can now delete an entire directory tree (including any files) using
the new "/s" parameter.
Examples:
RD "c:\somedirectory" ; deletes "somedirectory" unless it contains
; files or subdirectories
RD "c:\somedirectory" /S ; deletes "somedirectory" including any files
; and subdirectories it may contain
NOTE: Just as its commandline counterpart, KiXtart's "RD /s" command
deletes ALL files, including hidden, system and read-only files.
Use this command with great care!