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There is a known bug that stops rename working correctly if the underlying filesystem doesn't support hard links:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=308561

So unless you can have...

Have you tried:
cd remotepath
lcd localpath
put localfile
mv remotefileA remotefileB

Or to create a 'tempfile' with the proper name in advance (local), upload that and delete it when done.
...

One thing that comes to mind is the possibility for embedded <CR> and/or <LF> characters.
Can you create simple one-line files (manually typed, or carefully cut/paste) and verify that this is not...

awk 's != FILENAME && /pattern/{print FILENAME, $0; s=FILENAME}' file1 file2 ....
Or with gawk:
gawk '/pattern/{print FILENAME, $0; nextfile}' file1 file2 ....

perl -e 'use POSIX qw/strftime/; @x = split /\//, $ARGV[0]; print strftime("%a", 0, 0, 0, $x[1], $x[0]-1, $x[2]-1900)' "10/22/2012"