We would suggest using either the SkyDemon Beta (via Testflight) or the normal public version, not both at the same time. I didn't think it was actually possible to have them both installed at the same time on a device.
Currently we don't support flagging a log as coming from a simulator, but we know some people would like that. Therefore next time we enhance our track log format it's likely we will include this feature, but I have no date for that.