I, too, have this problem of notes not being saved. I reported it to Ancestry and received an email saying thanks and we'll try to get that fixed. That was months ago. Meanwhile, as a work around.......immediately after entering something in the note field, quit the program before you click anywhere else and your note will be saved. This is not a very satisfactory solution but it will work until they get it fixed.
I like a lot of things about FTMM2 but I'm done with it now, tired of all the many bugs. It feels like second class software. The last straw for me was when I launched the program and it informed me that my family file (and all it's media files) are no longer linked to Ancestry! This happened once before and now I have two trees on Ancestry that are identical. I don't want to go that route again. I've had enough fun!