Hi Blazej,
There are definitely no other instance of Stardog running. The JVM has not been updated. OS updates were applied on December 25th, but the Stardog service (1.1 at the time) was restarted without issue. JRE6 and JRE7 are both installed on this machine, but it's been like that for a while and it's JRE7 that Stardog is using.
That said, I think I've fixed my issues. I noticed that when I started Stardog as a service it was no longer creating the lock file. It looks like this was a permissions issue; the service no longer had read/write access to the Stardog folder. (maybe the result of me recreating it) So I set up the service with a user account that had permissions and Stardog was able to start properly. I was able to connect to it via HTTP at port 5822 and stop it normally.
This does raise the question of what was Stardog doing when it was started and didn't have permission to the directory? In subsequent restarts I wasn't getting any errors in the log files. I'm guessing the Java process was stuck at some error or warning but it wasn't getting logged and the service manager thought it was running normally?
I'm still not entirely sure what happened to cause all of this... I've been running Stardog and applying updates like this for months without any issue, nothing has changed. But I have seen many cases where all by itself Windows seems to make unexplained changes to security or files, so I'll just write this off as that.
Thanks!
PS - What's the proper way to set what port you want the service to start at? I must have done it before, and I know how to do it from the regular command line, but I'm not sure how to do it for the service and I don't notice it in the docs.