I don't know if it is any indication of whether or not changing the plugin to use the "run event" command will work or not, but it didn't fix my problem to have xremote trigger a "run event" of my ir events. I thought that maybe that way the wait commands would be used in the second event since they are being run by xlobby instead of the plugin.
in this case, run event is useless even if used from XRemote
I think that you better have to introduce a bug to Steven.
Such kind of problem must be resolved in the core (calling an event from run event should have the same effect that calling the event directly)
When Steven introduced this command I made a warning regarding the threading issues, but no answers.