While 0.8.6 improved this a lot, I am still getting some significant slowdown in some battles that take a long time (a significant amount of Instability 5 realms with lots of defensive mods for the creatures, for instance). I think it is still related to Elemental Tome or the creation of ethereal gems during battle due to cabalist traits.
Approximately how many spell gems are you creating in battle? Hundreds?
It usually starts happening at about three pages or so. Stat changes also seem to play a factor.