I'm reasonably sure that Mike Snook's Go Strong into the Desert describes them as using flags of differing colours describe the 'units'. Examples (from the top of my head) include, The Red Banner, The Black Banner.
The three "flags" at this time were the armies of the three Khalifas under the Mahdi. The Black Flag was the Khalifa Abudullah's force from western Sudan, the Red Flag was the Khalifa Muhammed al-Sharif's force from the Nile region north of Khartoum, and the Green Flag was the force of the Khalifa Ali-an-Hilu from the region south of Khartoum.
Osman Digna and his Beja don't seem to have been part of this organisation and he is not mentioned as being a Khalifa or having a flag colour at this time. It seems individual unit flags were manufactured in Omdurman and generally kept there, along with the firearms and artillery the Mahdists had accrued. Digna's relative distance and isolation from the rest of the Ansar may well have meant they weren't issued any flags. Their firearms had been acquired in their own local victories, so it may be that they weren't part of the main Ansar supply chain at all.
Fripp's painting of Tofrek does indeed show a white banner with coloured Arabic lettering on it, but as Ozwarrior says, this may be artistic licence. Skimming through my books I am yet to find a specific reference to any flags. I need to see if I can find my old copy of "Fighting the Fuzzy Wuzzy" by E.A. De Cosson, as it is an eyewitness account, and see what he has to say. Unfortunately I'm not quite sure where I put it.
