You could try exiting emulation station the using “top” to see how much CPU is being utilized by other processes. Give it a second to settle from the intitial launch of top and take take a look at the top processes in the list. They shouldn’t total more than about 1%.
If there’s nothing occupying CPU then my guess would be it’s a performance issue that was always there, but you might not have it experienced it yet (or noticed). I’ve definitely observed roms have slowdowns in certain areas where it’s not consistently reproducible. Your perception of performance can also be influenced by expectations, so it’s hard to be scientific with these types of tests. You could try turning on a fps display to see if it drops (not sure if mame4all has one).