Earlier today, we mentioned that Carlos Rogers had seen his $5.5 million base salary guaranteed as of April 1. Later in the day, Matt Maiocco reported that $1.25 million of his $5.85 in total salary ($5.5 million base, $350,000 in bonuses) had been guaranteed. Now, late this evening, Pro Football Talk says they have a source confirming that only the $1.25 million is guaranteed for skill and salary cap.
Where does the confusion lie? PFT's article mentions the contract being signed in November. Rogers originally signed his deal last year as a free agent, but re-negotiated the deal in November so the 49ers could extend NaVorro Bowman. As Matt Maiocco reported a year ago, the $5.5 million did have a full April 1, 2013 guarantee when it was originally signed. However, there appear to have been some changes when Rogers and the 49ers re-did the deal during the season.
As with anything involving NFL contracts, a vast majority of the information is hidden in secrecy, and we are all left to "sources" for information on the deals. While we can never be 100% certain of any of this information, we do seem to have some measure of clarification on the issues with Carlos Rogers contract.