It sounds like it simply needs more heat. I heat sometimes to the melting point then back off. Maybe your heat gun is getting weak, or not getting as hot as it should. I've had heat-guns go out slowly, where they just won't get hot enough. It takes a good bit of heat to shrink film... I'd try cranking your iron up, find the point that it melts the film, then back off a touch. I've heard stories about Monokote changing over the years... I'm not quite sure I believe them though, as I've never had any trouble.. and I've recently bought and used new Monokote for a few projects.

Sometimes with film covering, it takes what it takes... as there are variables that come into play, such as environment(we are dealing with heat-sensitive material), the structure being covered(open bay or solid), even down to the tools being used... and I'm not saying anybody else is wrong, or that I'm right here.. but these are all possibilities you might consider.. I wish you well.