My GUESS is that the new owners were keen to start with a clean slate which meant severing all links with previous regimes at the club - including those organisations that held said regimes to account.
I would venture (again, pure guesswork) that the club made it clear to the people running The Saints Trust that it was a link with the past and that they wanted to use different communication channels to communicate with the fans (e.g. More emphasis on 'official' announcements via the OS and more personal 'dinner with Cortese' events).
The Saints Trust probably disagreed with this stance and thus things headed down the 'tit for tat' route...(SFC: "please remove affiliation with club from your website"; Trust: "we're complaining through the press about your season ticket plans"; SFC: "if you don't like it we won't sell you one then"....blah, blah, blah...
If the above is anywhere close to the gist of it then I'm pretty sure NI would have had a season ticket if heels hadn't been dug in to keep a (some would say) 'without mandate' organisation going...
None of this is my opinion nor is it observation of fact. Just putting a theory out there which may or may not be near the mark.
For what it's worth, I tend to agree with the club in principle (i.e. That the Saints Trust served a purpose when the club was a plc, but not now) but also tend to agree that the way they apparently handled it was poor (I believe Cortese admitted in his December BBC interview that all communication last summer wasn't up to scratch, for obvious reasons)