Almost couldn't believe your statement that it is working.
So I went and downloaded the latest 2.4 beta build (dated 06.05.2017).
And indeed this one now works.
Some FreeBSD fixes must have been applied this past week to the pfSense build.
Just for clarification:
pfSense 2.3.x never had a problem with 2012R2 (as far as I know), only with 2008R2. This is a FreeBSD 10.3 bug that still isn't fixed, at least to my knowledge. (unless the fix is to go to FreeBSD 11+)
pfSense 2.4 Beta had a problem with 2012R2 (did not test with 2008R2). This was a FreeBSD 11.0 bug. I read on the FreeBSD forum, that it was fixed in 11.0 stable p8 (or something like that). It seems pfSense has now picked up that fix and all is well :)
2008R2 might be considered "old" by some, but there are still a lot of servers out there with it and it is still supported by Microsoft (albeit only the Extended Support cycle).
And it's not like anyone is going to splash out 1000+€ for a new Windows Server license just to upgrade for the sake of running a newer pfSense version.
Not to mention that the server motherboards might not support a newer Windows Server version, which would require a huge amount of money to upgrade…
Anyway, the underlying problem seems to be fixed now, making me one happy puppy :)