Do you see anything in these other keys?
HKLM\System\CurrentControlSet\Control\Session Manager value: PendingFileRenameOperations
HKLM\Software\Microsoft\Windows\CurrentVersion\WindowsUpdate\Auto Update\RebootRequired
HKLM\Software\Microsoft\Windows\CurrentVersion\Component Based Servicing\RebootPending
HKLM\Software\Microsoft\Updates value: UpdateExeVolatile
The key you referenced for BESPendingRestart are the values put there though an “action requires restart” or “action may require restart” command in a Fixlet. These three values should all be cleared after a single reboot - if the BES Client detects that there are no other pending restarts. If one of those four keys/values above still has data, the BES Client detects a restart is still needed and does not clear the BESPendingRestart key.