Tighten the neck and it gains a flat plane relief (tightening it is CLOCK-WISE) Loosening the Truss-Rod (COUNTER CLOCK-WISE) will allow flex.
This is generally done with the neck in position and in many cases with string tension. It is also very important to do this at a 1/4 turn at a time (DON'T crank it; work in increments slowly and allow it to settle). Excessive Truss-Rod turning can result in problems. The work should be done in increments, slowly, and allowing for the neck to adjust in position. Remember his is a laminated unit under tension, etc. It's really never a good idea to turn 1/2 rotation at an adjustment sitting; this is very standard with virtually every major manufacturer.
Some fellows use 1/6th turn and wait well over an hour before turning again; some even wait over night or play on the guitar for extended periods. The point is that it needs to adjust.
There IS a possibility that the neck was shimmed. The best method is with manufactured shims (which are often metal and stamped with size #). However occasionally it's done with paper, cardboard, etc which has a tendency to "settle" or fall out unnoticed. Additionally there are necks that need to be in exact position and improper re-setting of the neck can slip over a wooden "thread" of the wood-screws especially if a power screwdriver is used (always use a hand-screwdriver).
A very important point here is that the wood used in a neck is almost always harder than that of the body. Therefore if the neck junction is not level flat (difficult to achieve is mass production occasionally) then the wood will press an impression that can be distorted if not placed back EXACTLY as it was set! Problems arising can be "appearing as warped", fret buzzing, and intonation issues.
Over tightening can lead to all sorts of problems; including what you are describing. It can also crack the finish or worse. The compression can certainly alter the mating of the neck & body. Replacement of the neck should be done very carefully with a hand screwdriver. The neck WILL be set strongly with hand torqued pressure. It should not be "cranked".
Back it out of there. Check for any evidence of a shim. Replace if necessary. Replace the neck with a hand screwdriver. Torque should be approx. 5-12lbs depending on depth & screw thread, string set / number, and width.
