It's not possible to train on a skill twice at 1st level
I checked for all references of proficiency, trained and expert in the playtest book, and there is absolutely no reference of a general rule that when you obtain a Trained proficiency twice in a skill, it increases to Expert. The only reference of such thing is on the Skill Increase (page 42) class ability that all classes get:
This section specifies the levels at which your character
can increase her proficiency rank in a skill. At 3rd level
and every 2 levels thereafter, most classes grant a skill
increase, though rogues gain them earlier and more often.
Your character can use this skill increase to either become
trained in one skill in which she’s untrained or become an
expert in one skill in which she’s already trained.
This, of course, could be unintended, as there are several ways to start with a character Trained on a skill from two sources, especially since the skill proficiency gained from your class is free. You can pick whatever skill you want when choosing your class, as the Signature skills are suggestions (page 42), though some higher level abilities will affect those more specifically, and you are generally limited to Expert proficiency in non-signature skills (page 144).
However, since picking those skills is a choice, it's not weird if you say that you are picking the skills you want to be trained at, so picking a skill twice wouldn't make any sense. Regardless, my searches at the playtest forums found no similar questions. Thought a few users mention that you cannot gain higher than Trained in a skill at creation(here, here, and here), which makes me think that this may have been mentioned or hinted by the developers on another media (paizocon or podcasts), or (most likely) they simply accepted what is written in the book as literal ("You are trained in X") and didn't consider it a possibility.
So, until further clarification, I would say that Hero Lab is wrong on this subject.