Since at least 1999, the money for the highly-enriched uranium supplied to the United States as part of the HEU-LEU deal went to a separate fund administered by Minatom (more or less without supervision). This practice changed this year – the 2005 budget law liquidated the fund and now the money for the separation work (as well as those for the “natural component” of the enriched uranium) go to the federal budget.
As far as I can tell from the budget appropriations, Rosatom then gets from the budget about 12.2 billion rubles (about $450m by the inaccurate measure of official exchange rate), of which about 5.1 billion rubles ($190m) is a direct compensation for the work involved in blending the weapon-grade uranium down, and the rest – to various Rosatom programs – from science (1.6 billion rubles) to safety improvements (1.5 billion rubles) to unspecified weapon-complex programs (3.9 billion rubles).
According to the USEC progress report, Russia has been delivering about 30 metric tons of HEU worth of low-enriched uranium annually. If we believe the USEC estimate that the total value of the enrichment component of the 500 metric tons of HEU deal is about $8 billion (another $4 billion is the natural uranium component), then Russia should be getting about $480 million a year for its enrichment services. It looks like Rosatom with its 12.2 billion rubles in appropriations managed to get itself a fair deal from the Russian government. Unless, of course, it used to keep the natural urnium proceeds in its fund as well.