BLUF: FMS appears to be sequencing the active leg too soon on large turns (greater than 45* turn) and defaulting to "direct-to intercept next leg at a 45* angle". This places the aircraft in an undesirable location for some departures/arrivals.
From your screenshots it appears that you're having the same problem I've been having with RNAV SIDs involving substantial turns (more than 45 degrees). It appears that the FMS is computing an excessively early lead turn point to make these turns, causing it to seem to omit specific legs of the departure.
My most recent example was on the GYPSM5 departure out of Eagle County (KEGE), the FMS turned the 215* course OK but then turned too soon toward KIRLE, turning into the mountain. While in this turn it then sequenced to RLG (approx 12 nm prior to KIRLE) so that it was turned to intercept the KIRLE -> RLG courseline. This of course also places the aircraft above/into terrain. With a westbound turn to join the enroute structure, the FMS again discontinued trying to get to RLG approx 14 nm prior to RLG, instead sequencing RLG -> WEEMN, turning around to try to intercept the RLG -> WEEMN courseline at a 45* intercept.
Recommend developers look at the lead turn coding, as the problem appears to start there.