Just for clarification, this is a list of Waynesboro captures from the MOC.

WD234- 2nd Nat. Earlys HQ flag
WD249- ANV type
WD250- Hosp flag entirely red bunting
WD251- ? ? ?
WD252- ANV type
WD253- Hosp flag red bunting
WD254- Va State flag
WD256- Hosp flag? entirely blue bunting
WD257- Hosp flag red bunting
WD258- " " " "
WD260- " " " "
WD261- 2nd Nat Fragment

Its pretty clear that the Valley army was using flags made of RD English bunting. The uniqueness of the hospital flags might indicate a source, maybe Staunton, that is supplying Earlys troops. I think this helps make sense of it all. Without depot records its all speculative.
Can anybody trace WD251? That would be an interesting clue.