On page 292 of the Dungeon Master Guide, Filth Fever is listed as a DC 12.
The Dire Rat entry in the Monster Manual says the DC of Filth Fever inflicted by such a beast is DC 11.
I'm currently ruling on the assumption that Filth Fever on it's own is a DC 12, but when inflicted by a Dire Rat it has a DC of 11; but I'd like to know if there's a better way to handle this discrepancy.
You are correct. Sometimes diseases and poisons have specific DC when carried by certain creatures.
The DCs are calculated differently. The Dire Rat's DC is constitution based. 10 + CON modifier. Dire Rat CON = 12 (+1 modifier), therefore DC 11.
When there's a chance of exposure to filth fever that's not dependent upon a creature exposing an adventurer to the disease, the disease filth fever typically requires succeeding on a Fortitude saving throw (DC 12) to avoid infection. That saving throw DC is used if the DM determines that the surroundings are so filthy that filth fever is present: "Those injured while in filthy surroundings might also catch it [i.e. filth fever]" (Dungeon Master's Guide 292).
However, the extraordinary ability disease of the dire rat (Monster Manual 64) has its saving throw DC computed like most creatures' special abilities are. The Monster Manual on Special Attacks and Special Qualities, in part, says
When a special ability allows a saving throw, the kind of save and the save DC is noted in the descriptive text. Most saving throws against special abilities have DCs calculated as follows: 10 + 1/2 the attacker’s racial Hit Dice + the relevant ability modifier. The save DC is given in the creature’s description along with the ability on which the DC is based. (6)
Thus the saving throw DC against the dire rat's extraordinary ability disease is 10 base then +0 for the dire rat's one Hit Die (rounded down) then +1 for the dire rat's Constitution modifier for DC 11 total.
While this does make the disease filth fever more dangerous to adventurers when it's present in the environment (Fort DC 12) than when it's carried by the typical dire rat (Fort DC 11), most of the time the environment isn't also trying to eat the adventurers. Most of the time.
This is an intentional difference in the 'lethality' of a disease depending on circumstances like on what creature carries it and their HD, just as various poisons from various creatures have different DC from each other instead of having the same DC whatever the creature is.
Here is a list with diseases and their usual DC: http://www.dandwiki.com/wiki/SRD:Disease
If a certain infection spreads you might want to use the usual DC for further infection rolls unless the creature specifies to use a different one when the disease spreads further than the original infection caused by the creature.
Your above example would mean: Dire Rat infection DC for Filth Fever is 11, if you rule that the infected themselves can also infect new victims it might be the usual DC 12, just as in case of "Those injured while in filthy surroundings might also catch it.". Injury infected diseases aren't usually contagious (exceptions exist) and ingested-type is probably only transmittable if you have an infected person preparing food.
