Have they ever worked on the ROM?
How does the ROM call root? Some ROMs call root via init.d - I'm not sure in this case if init.d scripts that run before that are causing an issue.
You can crate init.d scripts that don't require root. Thinks like:
echo "hello" > /sdcard/hello.txt
And check they can do that.
As for specifics, I'm not familiar with the rom or kernel.