What happened
The original project is made with Unity 4.1.0f1
- (1 case) -- when I opening it in 4.1 and then 4.3 and then in 5.0 and then in 5.2 and then in 5.3 and then in 5.4.0b4 - everything works ok
- (2 case) -- when I opening it directly in 5.4.0b4 - the palm's branches are different
- please see screenshots in comments

How we can reproduce it using the example you attached
1 - Open attached project (scene substance_bug) in 4.3 and then in 5.0 and then in 5.2 and then in 5.3 and then in 5.4.0b4 - everything ok
2 - Open attached project (scene substance_bug) directly in 5.4.0b4
3 - compare results you see - please see screenshots in comments