I have been playing a game for the last 6+ hrs. I have had 3 Freezes/Slowdown's.
It happens everytime once I hit the end turn, it involves my ships auto moving and collecting anomolies/settling worlds all in this turn. If I get to many pop ups one after the other due to this activity and do not deal with them as they appear the game will freeze/slow down, by this I mean even though the game apears to freeze it does not. If I mash the Enter key to auto select/close pop ups they will disapear 1 by 1, however, it takes around 45-60s for each one to close. After dealign with these the game is really really slow to respond, so much so its easier to just Alt+F4(which will take 45+ seconds to work) and reload a save.
I took a screenie during the last freeze/slowdown. No ticket sorry(unless you specificly ask for one), using Mods 
Edit:
Gigantic Map, 8 AI, Abundant everything apart from Extreme Planets which is Common. No Minors.
I also noticed the new turn counter bottom right by the Turn button disapear's on the odd occasion. Dunno if that is linked or not.