You will only be reimbursed for that part of your premises that the PCT accepts is being used for GMS (or PMS) purposes. If the PCT deems that the property is too large, or includes such elements as residential accommodation that are not needed for GMS purposes, then they will be excluded from the area it will reimburse for.
From what you say, I do not think that this is the problem and I believe you probably are receiving 100 per cent reimbursement.
A valuer does not look at the gross internal area but at the net internal area of the property. The guide valuers use is the Code of Measuring Practice issued by the Royal Institution of Chartered Surveyors (RICS), together with Valuation Information Paper 4 (also from the RICS).
The valuer will take the gross internal area and deduct all structural walls, WCs, 'plant' rooms, lifts, stairs and stairwells, together with areas of essential access or areas used in common.
If you are concerned about the way that the assessment has been done, you should contact a specialist valuation surveyor to advise you.
If your own valuer feels that it has been incorrectly calculated, the PCT should have local dispute resolution and will normally instruct the DV to liaise with your valuer. If that fails, you can make a formal appeal.