Ah, then there's your issue. If it never caused a problem before to not set the advised rank in a static campaign (DGen is a completely different thing!), then you are simply very lucky.
See, this advise about rank was given for a reason.
In Il-2 the word "rank" is kind of misleading. It is more of a "position in flight and squadron" setting.
highest rank: you are in the lead position of flight 1 in that squad. Always. No matter what the .mis file says.
lowest rank: Tail end charlie of the lowest flight in your squadron. Also no matter what the .mis files says.
Ranks in between: various wingmen positions and things like 2nd flight leader (if available)....
The actual rank name is just "show". You can even edit it to your own liking, the file is open in each county folder (for static campaign. DGen is different. The mission is generated around your choice there.) The game is really dumb in that regard in static campaign mode.
Add to this that if you start low, you will advance throughout the campaign (and therefore changing your position in the squad!) - but at an unpredictable pace, unknown to the campaign maker, depending on your scores....
And also add to that that the game dutifully ignores "AI only" settings for the player flight... your "rank" setting overrules this.
You see the problem?
Therefore any campaign and mission builder must take this into account and circumnavigate this behavior of the game by choosing his squadrons in the mission carefully, to make sure you end up in the flight you're supposed to be, particularly in heavily populated missions.
The only way to be certain where a player actually ends up is two things:
1)Advise to set highest rank: Player will always be 1st flight leader. He can't advance at random. That's the safe bet for a campaign maker and makes most sense most of the time.
2)Make player flight unique. No other flight of that squad in the whole mission: Player can chose any rank and will always be in one of the four planes of that flight. But you cannot be sure which at any given time, that depends on what the player chose. Sometimes that's possible if it's not important that the player commands the flight. Wingmen and 3rd or 4th in a flight can't give commands after all. You will also not have the luxury of commanding any flight but yours in case of emergency even if you are flight leader!
So, long story short: If you are advised to start with a certain rank by a campaign maker: do it, or you will run into the situation you just did