can you go to the tools->options menu and find the "debug window" plugin in the tree and set it to auto start when droid explorer starts. then restart droid explorer. Can you then paste the output from that window here.
I am having the same issue with the latest build on two different PCs both running Windows 7 x64 Ultimate, here is a paste of the Debug Console
[CommandRunner] adb.exe -s I8975354dcf3 shell busybox ls -lF --color=never "/"
[CommandRunner] ls: unrecognized option `--color=never'
BusyBox v1.16.1 2010-04-14 09:51:31 MSD multi-call binary.
Usage: ls [-1AacCdeFilnpLRrSsTtuvwxXhk] [FILE]...
List directory contents
-1 List in a single column
-A Don't list . and ..
-a Don't hide entries starting with .
-C List by columns
-c With -l: sort by ctime
-d List directory entries instead of contents
-e List full date and time
-F Append indicator one of */=@| to entries
-i List inode numbers
-l Long listing format
-n List numeric UIDs and GIDs instead of names
-p Append indicator one of /=@| to entries
-L List entries pointed to by symlinks
-r Sort in reverse order
-S Sort by file size
-s List the size of each file, in blocks
-T N Assume tabstop every N columns
-t With -l: sort by modification time
-u With -l: sort by access time
-v Sort by version
-w N Assume the terminal is N columns wide
-x List by lines
-X Sort by extension
-h List sizes in human readable format 1K 243M 2G