To rsync from Windows to Unix/Linux you should provide a command like
SET BACKUP_SERVER=my.backup.server
SET SSH_USER=theUnixUserName
SET STORAGEPATH=/home/%SSH_USER%/Backup/
SET STORAGEURI=%BACKUP_SERVER%:%STORAGEPATH%
SET SSH_ID=/cygdrive/c/Users/theWindowsUserName/Documents/keyfiles/id_dsa
SET EXCLUDEFILE=backup_excludes.txt
SET BACKUPLOGFILE=/cygdrive/c/Users/theWindowsUserName/Backuplogs/backup-%DATE%-%TIME::=-%.log
The ssh command then is
SET BACKUP=rsync -azvu --chmod=Du=rwx,Dgo=rx,Fu=rw,Fgo=r --rsh="ssh -l %SSH_USER% -i '%SSH_ID%'" --exclude-from=%EXCLUDEFILE% --delete --delete-excluded --log-file="%BACKUPLOGFILE%"
with backup_excludes.txt containing lines of ignored elements like
.git
.svn
.o
\Debug
\Release
Then you would use this in a script with
%BACKUP% /cygdrive/c/mySensibleData %STORAGEURI%
%BACKUP% /cygdrive/c/myOtherSensibleData %STORAGEURI%
%BACKUP% /cygdrive/c/myOtherSensibleData2 %STORAGEURI%
and so on. This will backup your directories mySensibleData, myOtherSensibleData and myOtherSensibleData2 with the permissions 755 for directories and 644 for files. You also get backup logs in your %BACKUPLOGFILE% for each backup.