but could not find a generalised solution or an explanation of why this is happening

Really? Only a handfull of things could cause "Permission denied". You either don't have correct access permissions (unlikely), or the directory is use (open dirhandle), or it isn't empty. Example

C:\>perl -e"mkdir 1234; opendir IN, 1234;rmdir 1234 or die $!"
Permission denied at -e line 1.


C:\>echo >1234\test

C:\>dir 1234
 Volume in drive C has no label.
 Volume Serial Number is 44B0-3C2E

 Directory of C:\1234

04/22/2006  03:49 AM    <DIR>          .
04/22/2006  03:49 AM    <DIR>          ..
04/22/2006  03:49 AM                13 test
               1 File(s)             13 bytes
               2 Dir(s)   3,360,935,936 bytes free

C:\>perl -e"opendir IN, 1234;rmdir 1234 or die $!"
Permission denied at -e line 1.

C:\>
[download]

Any help would be appreciated very much. Thank you.

Well it appears to be a bug in ppm (and maybe other things), so contact the maintainers of ppm, and maybe even search the mailing list and bug database.
http://aspn.activestate.com/ASPN/PPM/
http://bugs.activestate.com/PPM/query.cgi
http://aspn.activestate.com/ASPN/Mail/Browse/Threaded/ppm