Unfortunately there are some known lag issues with the game on certain computers that I was never able to really fix. The only workaround I was able to find is that if you save the game and restart the program, it should run normally for a little bit (before slowing down again;;).
However, I've never heard of the beginning portion of the game being laggy (just the puzzle portion) and if the game was still laggy even after restarting your computer I'm not sure what's causing that. Maybe see if you have the latest version of DirectX installed? (https://www.microsoft.com/en-us/download/details.aspx?id=35)
Sorry about that!