They haven't run out of money, but funding will not be available for a short period of time after the new fiscal year 2012 (which starts October 1st). During this temporary lapse of funding, they will still be issuing conditional commitments "subject to the availability of commitment authority" and lenders are still fine to close this loans as scheduled, however USDA will not "obligate" the loans until funds become available. This means the lender will assume all default risk (and not sharing it with USDA) until the funds become available.
What does it mean to you, as the consumer? That because the lender has to assume all the risk, there may be some lenders who will shy away from funding loans until funding becomes available again, which from my discussions with a few different USA offices has been anywhere from a week to 2-3 weeks. Shy away could mean stop funding them all together or only funding a certain dollar amount (i.e. $50,000,000 in USDA loans for conditional commitments which have that "subject to" verbiage). There are many lenders who have indicated no interruptions are expected with their USDA loans.