I use the forums in different virtual machines and no problem, the instances of host and guest are completely separated, the thing you might be sharing - depending on if you use NAT/Bridged connection is the local network IP.
Personally I think the problem is elsewhere.

Things that can make differences
- Are you logged in on one and not logged in on the other (not logged in you can have a different thread preference)
- Once I logout on one it will tell that it "cleared all cookies", so threads are no longer marked as unread.
- You mention Chrome, so you might be using plugins that block javascript or ads (yahooapis.com is apparently used, not required for the way I read the forums, but it might be for yours)
- Make sure Chrome is actually on the same version for both, although I would not expect it to be a problem.
- Are you using custom CSS? If so you might want to remove that.
- Did you change your default User Agent? (Has bitten me before when I had set it to be the same as a search engine robot as the site in question served things differently)
- Using a proxy could make a difference, but I doubt you are using that.

It's a windows 8.1 thingy, reboot (just kidding, don't think it is going to help)