Why does script execution take twice as long on a server?

I'm assuming you're running TC 12?

One main thing to try is, on your 2012 box, in TC/TE, go to Tools | Options | Engines | General and turn off the option for testing Windows store applications.  Restart TC/TE and see if that helps.

Another thing to try and this is probably not related to the 2012 box but to the installation.  By default, under Tools | Options | Engines | NameMapping there is an option for "Search for visible objects first".  That is checked by default on a new installation and does actually slow down execution somewhat.  Try unchecking that option and see if that works.

I personally haven't noticed a major slow down in 2012 server execution with these two settings (we have them by default in our envioronment turned off).  Give this a try and see if it helps.