Does shakeup in 49ers' front office loom?

Not everything is adding up in San Francisco after a report late Wednesday night that 49ers general manager Scot McCloughan was considering resigning his position.

Matt Maiocco of the Santa Rosa Press Democrat reported that McCloughan met with the team’s leaders earlier in the day and that he ultimately left the club’s Santa Clara facility and files were “relocated from his office.”

"Scot McCloughan is not resigning as general manger of the the San Francisco 49ers,” McCloughan’s agent Peter Schaffer told the Sacramento Bee.

That doesn’t address whether or not McCloughan could be fired from his post, but it casts at least some question over the guidance of the franchise as the secondary free-agent market continues to churn and the draft approaches quickly. The Niners own two picks in the first round and it’s going to be a critical draft as they attempt to make a large stride forward in an NFC West division that is wide open.

Maiocco reports that McCloughan huddled with Jed York, the owner, vice president of football business operations Paraag Marathe and others including Michael Rossi, a retired banking professional who serves as a senior advisor to the franchise.

The 49ers haven’t always handled things in the smoothest fashion. In a league where everyone tampers and no one gets caught, the Niners got caught with their hand in the cookie jar. They were found guilty of tampering with Chicago Bears linebacker Lance Briggs and forced to forfeit a draft pick and swap picks with the Bears. That happened closer to the beginning of McCloughan’s run. He was originally hired as a vice president of personnel by former coach Mike Nolan.

Stay tuned. Surely some answers have to come out of this situation.

Follow me on Twitter: BradBiggs