Have You tried do that from shell?? Best from root account??

Maybe on server there are some specific rights to libraries
or to keys that does not allowing them to be opened by
webserver user or just does not know where to look them
or maybe xmlsec1 can not open or write files ??

I know it would be stupid but..... it sometimes happend :-)

Try from shell:

copy xml temp file to somewhere ex. /tmp/testfile.xml

/usr/local/bin/xmlsec1 --sign --privkey-pem /path/secured.key --
output /tmp/testfile.out /tmp/testfile.xml

I do not even ask if You have correct privkey file :-)

Look here: http://www.aleksey.com/pipermail/xmlsec/2007/003988.html

Aleksey suggests that "Something is wrong with your default
certificates directory."
http://www.aleksey.com/pipermail/xmlsec/2007/003989.html

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