I have had a few tranny problems. Not the same symptoms, but when I had my yz125 stuck in gear, and another time had my kx250 stuck in neutral, I was able to see the issue while the cover was off. Its possible to have something assembled wrong just like it was before, if your mechanic is a visual learner and just put things back as he found them.
Does it shift from neutral once and then hard to shift? There is a flat metal slider-deal in there that actually rotates the drum. if that deal doesn't return properly it causes issues. Also, if the drum makes an incomplete rotation, the next shift hits a corner of the drum, ect. ... that could lead you to what it's not, for sure. Someone will need to visually inspect the operation, to get to the bottom of it. Hope you didn't pay much to get it back in the same condition...