Dear Josef,
I think I figured out part of the problem. There was an issue with the keys which were missing the proper extensions (windows just shows <all> and ignores what is in the cert). Having fixed this, I can see all aliases property, but now I run into another problem.
I use a property files with "--load-properties-file" where some of the entries are set, e.g. position of the visible signature etc. When I include this option it uses the wrong cert, when I do not include it in the command, it works fine.
The properties' file reads
crl.enabled=false
hash.algorithm=SHA512
ocsp.enabled=false
ocsp.serverUrl=
proxy.type=DIRECT
proxy.host=
proxy.port=80
signature.append=false
signature.location=XXX
tsa.enabled=false
tsa.url=
tsa.user=
tsa.serverAuthn=NONE
tsa.cert.file.type=
tsa.hash.algorithm=
tsa.policy=
visibleSignature.enabled=false
visibleSignature.render=GRAPHIC_AND_DESCRIPTION
visibleSignature.acro6layers=true
visibleSignature.img=Sign.png
visibleSignature.page=999
visibleSignature.llx=150
visibleSignature.lly=10
visibleSignature.urx=425
visibleSignature.ury=50
visibleSignature.l2textFontSize=6
so there are no settings regarding the keyalias. these come with the paramters such as
jsignpdfc --load-properties-file "Sign.ini" --contact "Admin, Test" --hash-algorithm SHA512 --key-alias Test1 --keystore-type WINDOWS-MY --out-suffix "_signed" File1.pdf
Any idea? Thanks
Best, Holger