Totally understand this, although I definitely don't recall seeing a charge for education use previously; this may just be an innocent error or oversight on my part, though from your reply this WAS a change in policy. It would have been in 2013 when we first started using this, as a replacement for Game Maker Studio, whose developer, YoYo Games, intruduced an unacceptably expensive site licence fee. Interestingly Unity also did this a year or two before, causing many MANY universities to drop what had been a great free resource from their programmes ; something that they later regretted, and have since recanted on, due probably to major competition from Epic Games' Unreal Engine 4, which is totally free to all, and provides source code access to registered parties.
I would not knowingly have been using the free version on our undergraduate course if I had known that a charge had since been introduced. I have instructed our technicians to remove the software now, and will have to find an alternative 'low programming' entry game engine. This is a shame, as many of them do go on to set up SMEs and work as Indie or Freelance game developers, and likely might have become full licence owners. However, in the current climate, my institution cannot afford additional software licence fees, and we are being strongly encouraged to avoid all but the most necessary expenditure.
I'll carry on using Stencyl, of course, as I have legacy web apps that require this, and I genuinely like the engine for simple projects of my own, but I'll have to say goodbye to it as a teaching platform now. This is regrettable, as the abstraction layer, allowing novice programmers to create games with little or no coding experience, along with Haxe running underneath to allow them to stretch and grow into more specific programming of novel elements needed in more advanced games, was a perfect platform. We (well, they really!) produces some quite interesting games, and many of the students were able, due to the free web version, able to carry on refining their initial prototypes, developed from scratch with no previous experience in just 6 weeks; really only about 4 weeks of actual development time, and approximately 20-40 hours at most of programming time, similar to a sprint or game jam. One more task for my busy Summer now, is finding an alternative. I'm sure they are out there, but I will miss using Stencyl in more than a personal capacity.
DoctorMike
EDIT: According to the wayback machine, the link page
http://www.stencyl.com/education/pricing/ has only existed from December 2014, so presumably that is the first time I could have been aware of potential charges. Sadly, I note the price for a site licence then was $149, but only for the FULL version, and the page talks about free plans too, so you didn't even really charge for the web based version for some time. March 24th 2015 is when the free version became an 'evaluation' version. And I also note the price change on March 4th 2016 to $299 for even the basic version and $499 for the Studio one. I don't think these changes were communicated well enough.