What are the specs of both machines? (Especially CPU(s), RAM, and OS version)
Are they both running version 188.8.131.52 of After Effects?
When you say "slower", do you mean the interface, workflow, or final rendering?
Since this is your first visit to the forum, you might try searching for similar issues with the MacPro machines. We've seen several threads since they were introduced late 2013. Most of those threads end without any solutions.
I cant help you directly, sorry. My MacPro bogs down a bit with AE when certain network activity is running in the background but overall I'm quite happy with the performance. AppNap is mentioned in some threads about FCPX running slowly on the cylinders.
If you get it figured out, please consider posting your solution since hardly anyone ever does that around here.
Without specs and seeing your settings in Preferences for AE, cant really help with any fixes or answers. Keep in mind the nMPro is the Ivy E platform ie I7 Gen 3 and Intel has already moved to Haswell E I7 Gen 4. That is the X99 and Dual Xeon platform on PC with DDR4. The performance for AE is far better there than Ivy E besides the differences with OSX and AE.