An MRI taken on Luebke's elbow Friday revealed a tear in his ulnar collateral ligament. The 28-year-old also missed the 2013 season after undergoing Tommy John surgery in May 2012.
"I guess the general consensus was the graft never took and that there were some problems from the get-go," Luebke told MLB.com on Tuesday night. "Kind of the way the process has gone ... the stops and starts, and every time we turned up the volume and intensity, it was never too long before we had a setback. That sort of let me know there's something going on.
"My gut feeling through the rehab process was this didn't seem right. And when we did the MRI, it was pretty clear what was going on."
Luebke, a first-round pick of the Padres in 2007 out of Ohio State, broke into the major leagues in 2010. His first full season for San Diego came a year later, when he appeared in 46 games (17 starts), going 6-10 with a 3.29 ERA while striking out 154 batters in 139.2 innings.
The following season, Luebke made five starts for the Padres, going 3-1 with a 2.61 ERA before being shut down due to the first elbow injury.
"I feel bad for him ... from 2011 through the first part of 2012, he was certainly on his way," Padres general manager Josh Byrnes told MLB.com. "This is a real setback. There's been a lot of missed time. Hopefully in a year or so, he can get back to being Cory Luebke.
"This whole thing has been a mystery."
Luebke signed a $12 million, four-year contract in 2012. The deal has team options for 2016 and 2017 that could make the contract worth $27.75 million.
Manager Bud Black said it looked like the graft didn't take in Luebke's first surgery.
Had the first operation been a success, the Padres planned to ease Luebke back and would not have had him penciled into the rotation early on.
"Cory would have been a bonus," Black said Wednesday. "I think the world of Cory. I think the world of his ability, his stuff, his heart, his guts. If he had come back, it would have been great. ... You look at the numbers on the Tommy John, there's a 15-20 percent number in there that guys don't come back from that surgery, and Cory unfortunately fell into that group."
Said catcher Nick Hundley: "It's bad news. Cory's a great guy. It's tough when a guy does everything he can to get back and something goes wrong. It's tough for us as a franchise because he could be the face of the franchise. He's that good, that quality of a guy. You could literally hang your hat on that kind of guy. From that standpoint, it's tough, but he's resilient. I was with him when he got the news. You hope for the best for him. If anybody's going to come back, it's Cory Luebke."
Also Wednesday, left fielder Carlos Quentin said his legs feel much better heading into this spring training than they did at this point last year. He had surgery on his right knee late last season after being limited for a second straight season. It was his third surgery on his right knee in 18 months.
The Associated Press contributed to this report.