Weird lag in minecraft 1.9 but no FPS drop

Whenever I was in pre release 4 I noticed a weird lag similar to if I had too many command blocks running. I kind of forgot about it because I went to pre release 3 to work on commands. To explain this lag:

I pick up items very slowly, mobs move slowly when punched, grass takes a while to break when the block under it is broken, command blocks take a while to load when right clicked on (the command is blank and all of the buttons are black).

Now I thought this was surely fixed in the complete release of 1.9, but I just loaded it up and It has not changed. I have no FPS drop and my memory consistently stays around 20. I don't think this is just for me because my friend also experienced the same issue when joining my world. I have tried setting all my settings to low and It did not fix anything.