I know Dave is checking into this but one thing I noticed is that you were departing from a field that had a Ground frequency and you got clearance on the default FSS frequency. You were prompted to switch to Ground frequency (Ground handles Clearance functions when there is no Clearance frequency).
7/4/2018 11:14:48 AM: 290 - FS Screen : ComFreq: 122.2 <> GroundFreq: 121.75
If there is a Ground frequency and no Clearance frequency, you get your IFR clearance by tuning Ground and pressing 0. If there is a Tower frequency and no Ground or Clearance, you get your clearance on Tower frequency in the same way. Whether or not this has anything to do with the problems that followed, I'm not sure.