Hi,
just a suggestion for you, you will have to confirm for yourself whether this is the problem!
The FS7 has a problem such that if you normally have it set to CineEI/SLog*, then switch to Custom mode it will change some settings but remember the SLog2/3 setting.
You can confirm this by looking at a clip you recorded in Custom Mode in Catalyst Browse (or similar software that can read all the metadata on the clip). It will let you know what format the clip was recorded in.
If this is the problem, the best solution is to set the camera to all the Custom Mode settings you require, then save that configuration using the FILE MENU > All File and name that configuration as your custom format. Similarly do one for CineEI.
If you post a small clip somewhere I will have a peek at it.