I suspect that the modifications that the R.E.D DLL mod makes to unit scale and composition effects the units that the game loads since units that CEP depreciates appear.
Did you try the modinfo changes I outlined
here? If loading the RED mods first doesn't solve the problem then the compatibility problems lie deeper.
The R.E.D. dll for the Combat mod doesn't actually have anything to do with the R.E.D. unit mod. It's a derivative of the dll from the WWII mod. The unit mod is strictly data and lua (along with the art resources). Those work fine with Cep.
I did have Cep and CSO going together with an earlier version of Cep (last week or so), so the trouble likely lies between some new feature Thal added after v3 and some component of CSO and the RED dll (which hasn't changed).
I got the same results earlier when I tried your suggestion with the references, but didn't have time to fiddle with it too much. Going to try it with the dll as a dependency. Beyond the tagging, I suppose we'd have to examine the source and the relevant part of Cep.
It would be nice to get these two to play together at some point. I absolutely love the Combat Stacking Overhaul. Aside from being fun, it solves a lot of unit logistics problems by allowing peaceful units to occupy the same tile. It also balances long games by letting you build more units (without having to render all of them).
edit: Your other suggestion (the additional nil value check in GetUnitSortPriority) does solve the broken queue, as hellagrant mentioned. I now see that those 3 modern units are immediately available for build. Have to look more closely at how Cep is removing those. Are those the only deprecated units?
edit2: After peering into Communitas' data changes for combat classes, statistics, unit costs, etc... balancing these two would make for a pretty ambitious submod project (small technical incompatibilities aside). The impact of stacked combat and the required lowered unit costs (to get more units on the board) aren't to be taken lightly. Gedemon's mod is experimental at this point (though functionally, it's working quite well). Balancing, which is preliminary, is derived from vanilla statistics. I'd say it would be wise to wait until both mods (particularly Cep) reach a more mature state before going down that rabbit hole
Despite that, it would still be nice to locate the current conflict.