Simplest answer is outside of perl, since this seems to be a windows command shell thing. Before, 
C:\cygwin64\bin\rsync.exe -ashv -e plink --exclude=aide.log --exclude=
+aide_error.log weaverw@10.3.30.149:/var/log/aide

[download]
worked. Now, 
C:\Users\IBM_ADMIN>C:\cygwin64\bin\rsync.exe -ashv -e plink --exclude=
+aide.log --exclude=aide_error.log weaverw@10.3.30.149:/var/log/aide
Unable to read from standard input: The parameter is incorrect.
rsync: safe_read failed to read 4 bytes [Receiver]: Connection reset b
+y peer (104)
rsync error: error in rsync protocol data stream (code 12) at io.c(276
+) [Receiver=3.1.1]

[download]
But in general, it would be nice to execute scripts from within a perl launched by the usual windows command.com but with the environment of cygwin.

In reply to Re^2: Running a cygwin command from within activestate by WoodyWeaver
in thread Running a cygwin command from within activestate by WoodyWeaver

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