Thank you for the report, we're already aware of the issues present with the plugin and we're currently looking into a fix for the problems, although there is no ETA.
Without going into too much detail, the problem stems from the fact that the plugin is poorly designed and was not meant to run at the scale we operate at, and modifications to the plugin to allow it to do so were not without their drawbacks.
In the mean time, if you protect something it manages and you leave the area for at least 60 seconds (as in completely leaving the area by going to spawn, the mall, etc), when you go back to that new horse, it should store/summon/tp/etc as you would expect.