Your ABS guy is correct, assuming you don't have a single-process FCAW PQR to support your new WPS.  Did you write a new WPS for the FCAW-only conditions or did you just present a multi-process WPS to ABS for review? 
When using AWS D1.1, unlike in ASME IX, welding processes must be qualified individually and then combined to develop a multi-process WPS.  Extrapolating from that fact, your dual-process WPS is also not in accordance with D1.1 unless you have two single-process PQRs to back it up.  This isn't really clearly defined in AWS D1.1 but rather implied by omission of the clauses, and "thickness deposited" rules, you would find in ASME (for example) that do allow multi-process PQRs.  This is my understanding, at least.  I'm sure there've been many official interpretations on this situation if you have the resources to look them up.  Considering how at odds AWS and ASME are regarding the issue I would say it's not a silly question.
I'd like to hear other folks' experiences and interpretations of this as well.

Bigmac,

WELCOME TO THE AWS WELDING FORUM!!

Let's add just one thing to this as I am getting ready to make my daily 100 mile commute to Phoenix for my night job.

You say you have a PQR using two processes; GMAW root and FCAW fill and cap.  But then, you ask about only using one process but using a ceramic backing. 

Personal opinion is that the ABS people object because for D1.1 you have just changed something that is not prequalified per D1.1: cermaic backing.  Only steel backing is prequalified for left in place backing (which you did not specify if it is or will be removed).  Now, the technical interp is that other backings may be used if they are to be removed and the weld cleaned by grinding, chipping, etc and backwelded.  If it is to be left in place you need to do a PQR and then write your WPS. 

Remember too, in D1.1 you can't do an open root joint, no backing, unless backgouging and welding from the opposite side is involved (then it is not truly considered an open root) unless you have a PQR and WPS's that show the ability to satisfy the engineer's requirements for the job while completing the joint that way and meeting applicable code requirements. 

Now, it is interesting that he says your joint must be done with dual processes.  Not sure he is really up to speed with D1.1.  First, is your GMAW spray arc or short arc?  Short arc is not allowed without PQR's specific to the job in D1.1.  And that is what is often used for a root when incorporating GMAW with another process.  Low amperage to close up the root opening to create a 'shelf' for the following passes of the other process without blowing through. 

If I remember correctly, there is an article that addresses some of this in a fairly recent edition of...The Welding Journal?.  I'll see if I can find it and reference it later tonight.  You can find them on the AWS Website using the Website button at the top of the forum page even if you are not a member. 

He Is In Control, Have a Great Day,  Brent

Welding procedures used on ABS-certified equipment are usually pre-approved before use through a design-assessment and/or project kick-off meeting.  Crap does happen where new procedures need to be developed mid-job but they still typically go through a review process prior to use.  Not all ABS surveyors are well-versed in welding procedure qualification but it's not often that one who isn't highly qualified to approve WPS's makes a unilateral decision to reject one.  It's likely that he's standing on solid ground and can justify his decision.  That being the case, have you asked him to provide justification for rejection?  That would be the easiest way to clear up the issue.  His objection probably is not that the joint must be multi-process or that you can't FCAW on ceramic backing.  From the information you've provided it sounds like your procedure is simply just not qualified to AWS D1.1 requirements.