Just gave the horse rig setup a small test run. It all works well over here. I added an Abs layer, animated in it, shut it down and turned it on, all well.
However I use the base pose only for rigging and setup purposes. If you have started posing your rig for animations and then added an Abs layer, then yes, it all start behaving very dodgy ;), so you may want to start from scratch
If you want you can setup a horse rig relatively quick:
-Create a CAT Parent object and add a pelvis from its sub menu
-Select the pelvis and add two leg, add a spine, select the end piece and add another two legs and spine
-Now select the second spine and add a bone as your head
-select the first pelvis and add a tail
Just remember to position your bones (rotate position and scale and use the copy and paste limb settings) during the whole process. Otwerwise it wont look like a horse but some weird abomination 
Cheers
Chris