Is it normal to preferentially invite female speakers when there would otherwise be few female speakers?
First of all: if the women who were invited to speak are in fact highly qualified for this invitation, they are not getting a "free pass". A "free pass" implies that they are invited only because they are women, and are not otherwise qualified. Qualified women are at best getting a "priority pass" to make up for being often overlooked (especially when the organizing committee is all male), and possibly not getting any kind of special pass.

It is a bit insulting (although I am sure this is not your intent) to suggest that these women were invited to speak because they are women, and not because they are doing quality, competitive work. I can see why you were uneasy when the organizers sent an email emphasizing the gender of the speakers, instead of their contributions to research; I would also be. 

Second: depending on the sample size, it may not be entirely significant that 31% of invited speakers were women when they made up 18% of the list of suggestions.

In answer to


  Is this normal practice in academia:


Yes, sometimes a conference or workshop organizer will look at the list of invited speakers, see that women are heavily underrepresented, and think carefully about whether there is a qualified female researcher doing excellent work who could be added to the roster. 

This is done as a deliberate response to counter a known bias. We know that we (as humans) are very bad at evaluating people based on merit alone; we tend to let our cognitive biases get in the way. (See, for example: Science faculty’s subtle gender biases favor male students.) Deliberate attempts to increase the representation of women in underrepresented fields exist to counter this known bias.