Also, manual saves don't seem to be working. I reloaded the page to get rid of the slowdown and lost 10 prestige points even though I clicked save just before I reloaded.
The CPU is actually devoured by Stencyl physic engine (Box2D). It is part of my fault since I used it a bit much, and now I am having a bad time going back as it breaks many things. So I am doing it bit by bit.
Unfortunately slowdowns causes to delay on saving system. I'll fix it as soon as possible.