What version of beats are you using? 6.2?
Because I see an issue with the logstash configuration you shared. The index name is wrong:
It should be:
index => "%{[@metadata][beat]}-%{[@metadata][version]}-%{+YYYY.MM.dd}"
In your config, version is missing and also you have a leading slash, I think that is a mistake.
About the error with winlogbeat.exe, I don't understand as you said it was working now. Maybe when you run it by hand its using a different config that doesn't have the verification_mode: none change ?