According to the original source of TBBT renewal news Deadline Hollywood the focus of the negotiations was re-signing the original five. Once they were close to that goal they turned their focus to signing Melissa & Mayim.
Actually three things are happening at once...
Talent contract negotiations, license fee renewal talks between CBS and WBTV and negotiations for The Big Bang Theory prequel series, Sheldon, which is in the works for next season. (Lorre, Prady & Molaro will be involved in the prequel)
Also keep in mind as both Jim & Johnny secured WB production deals in the last round of negotiations, Johnny also has landed a pilot at CBS for a comedy called Living Biblically, which Johnny will executive produce.