I also have this problem - I just thought maybe there was only a chance for a harvest to give a jungle mushroom instead of all the time. I have the jungle mushrooms planted on tilled jungle in two rows nine spaces long each with one space between the two rows. The townie stands over the mushroom just like normal and then the mushroom turns back to a seedling and the townie walks off - doesn't drop anything and isn't carrying anything and if you right-click on them they have moved on to the next task. happens, maybe 1/3 of the time. Basically, it is acting like there is only a 60 or 70 percent chance to get a mushroom when you harvest a planted one.
Never thought it was a big deal since I plant lots of mushrooms. Also, I have always gotten a mushroom when my villagers pick a wild mushroom.
I'm positive that they are not taking it off to eat and there is plenty of room for them to set it down. I'm playing .47a and I have noticed this ever since planted jungle mushrooms were introduced - like I said, just thought it was supposed to be that way. Right not, one of my rows is right at the edge of the jungle, but in previous games I had the mushrooms planted right in the middle. Also, it doesn't just happen in a couple of spots - I have seen it happen in several places on both rows.
Hope this helps!