I'm not sure how much influence the Administratum and other factions which deal with the treasury have on a sector/planet's Mint, but perhaps a new currency was introduced when something stopped generic Imperium coin from being manufactured. Perhaps it became massively devalued and a new one had to be introduced in limited supply, or the Mint was stolen/destroyed by xenos/heretic invaders (possibly in an attempt to affect the war effort). This is of course talking about people who need them, and I doubt very much an Inquisitor needs coin to influence people when they can barter with their fists and psyker powers. Although that might not work with Rogue Traders of the Imperium! Unless they're incognito, like Eisenhorn sometimes had to be.

From a game design point of view one currency is great if you can keep it under control, but being an ARPG packed with loot to be vendored and credits being given as rewards, it's unlikely that will happen. Players will be flooded with them, much less considering the impact of the entire community trading and bartering. I would imagine more controlled currencies will be introduced for higher end players later on to purchase/craft better equipment later, so the devs could use some kind of excuse in the lore that this rarer currency is used to buy better stuff. ^^

Then again, neither could be true. It's just my opinion. The name could be a placeholder and the 'true' name for Imperium coin will be put in at a later date! ^^

The dark heresy pen n paper rpg calls imperial currency "Throne Gelt", or just Gelt for short.

Or just name them Credits - not like we would name our currency Milkyway Credits (probably copyrighted anyways) :D

"There is no monetary unity inside the Imperium." Straight from the Lexicanum

Lol cause it is an old sector and maybe that is just what is used there. Lore is not consistent even with GW so...

Source - Lexicanum