Hello shadwomage love your mod. works great with RP-1 now some examples for your great work in action https://imgur.com/user/Karlack26
I asked one of the Mech jeb devs in disscord about the issue i was having.
MJ auto staging does not like it when your insterstage, decouples form the stage below while staying attached to the stage above. Nathenkell eventually chimes in on the discussion as well on how MJ looks for decouples and the way your mod uses them may be the issue. here is the disscord link. The MJ dev posted a link to the relavent MJ code so you may be able to make some sense out of that.
https://discordapp.com/channels/319857228905447436/485125363253641228/551922167290527746
I am using KSP 1.3.1 so if this is a problem you have sorted out in later versions of SSTU never
mind. Just letting you know of this issue if its something you can fix on your end or if you can help the MJ guys change some thing on there end. But any who thx for your great work.

Thanks for the report -- I'll see if I can figure out what is going on. Likely not much that can be done though, as the ISDCs operate much differently than existing stock decouplers, and MJ simply isn't configured to handle them properly.