I think I know how to resolve this issue (it's a one shot work around though).
Create a new sequence and import the xml from the coroface creation.
Add all your display items.
Protect all the effects.
Go to bottom of sequence, insert the number of blank rows equal to the number of timing marks you have.
Start sequencing (random effects will now only fill in the timing marks and not the coro faces).
This still leaves sequencing VERY challenging without a filter to as I don't really sequence 800 or so lines, I prefer to keep my songs under 50 different effects.
Has anyone created a different approach to this, one thought was insert blank rows, create two sequences and cut/paste between the two.