Also, make sure you post any and all information from the crash notice and DebugConsole.txt file in your Cortex Command folder. Without more specific information on what errors you're getting there is basically nothing we can do.

Are you using 1.0 or B27 still? Which platform, Windows/Mac/etc.? Which version of the 40K-IoM Compilation?

ERROR: Tried to set an override purchase list with no delivery craft defined. Using a default instead.

CortexShock.rte/Scenes/Scripts/CortexShock.lua:2870: attempt to get length of field 'Logs' (a nil value)

I left Cortex Shock-specific actors disabled by default in order to cut down the loading times required. The IoM compilation is a large mod, enough that I was considering making the Cortex Shock functionality a seperate download.

Green refers to files in W40K.rte, and Red refers to files in CortexShock.rte.

1) Enable the chapter of your choice in Factions.ini - that's business-as-usual.
2) Open Index.ini and uncomment the line that includes CShock Index.ini.
3) Go into the CortexShock folder, open the CShock Index.ini, and uncomment the chapter(s) of your choice again. Remember you need to have the corresponding chapters already uncommented, or else it won't load at all.
4) Finally, make sure the faction .lua file is listed in the Factions.cfg of CortexShock.rte.

Might be wise to leave the faction .lua files commented out of the config file in future builds, since the mod can't easily determine which chapters are and aren't enabled; if any one of them fails to load due to not finding a specified actor, any following faction files will fail also.