Phil Mickelson left the North course at Torrey Pines four shots off the halfway lead held by DA Points and Ryuji Imada at the Farmers Insurance Open in San Diego.
World number two Mickelson had opened his season with a two-under-par 70 on the 7569 yard South course, while Scott Piercy's first-round leading 64 had come on the easier 6874 yard North course.
Mickelson had said he was looking to move into contention as he moved across to the North for round two and, while he did card a five-under-par 67 to move to seven under at halfway, American Points and Japan's Imada did enough on the South to get to 11 under par for the 36-hole lead.
Points was the most impressive, shooting a seven-under 65, while Imada took a 68, with another American, Matt Every, moving into a tie for third on nine under following a 70 on the South.
The relative difficulties of the courses made no difference to Points, who said: "Funnily enough, I've played this course a lot more than I've played the other one, and I feel pretty comfortable out here.
"The main thing for this course is obviously just making putts and driving the fairway, and those are two things that I've done the last two rounds, especially today I made a lot of putts.
"Iron game isn't quite as sharp as I would love it to be, but certainly making putts is always a good way to make up for a little bit of a sloppy iron game."
Australian Michael Sim joined Every at nine under thanks to a 10-under 62 on the North, with compatriot Robert Allenby part of a five-man group on eight under. Allenby shot a 69, with Americans John Rollins (66), George McNeill (67), Ben Crane (71) and Chris Tidland (71) alongside him in a tie for fifth.
Mickelson was also part of a five-man group, on seven under with 50-year-old Tom Pernice (71), rookie Rickie Fowler (70), Australian Marc Leishman (69) and South Korea's Charlie Wi, who shot a 66 on the North course.
Overnight leader Piercy had a bad day on the South course as he dropped to five under with a 75, alongside, among others, Ernie Els of South Africa, who shot a three-under 69 on the North.
Justin Rose of England climbed up the leaderboard with a 69 on the South to take him to four under, while a 70 on the same track moved Martin Laird of Scotland to three under.
Luke Donald stayed at two under following his level 72 on the North, but the same score on the South was not enough to get Greg Owen into the weekend, stranding him on one under par, the wrong side of the cut line.
John Daly was another to go home early, the two-time major winner's 71 on the North course not enough to dig him out of the mire following an opening 79.