I had the same problem on my '69 Cuda, 318, factory manifolds. After replacing the gaskets numerous times I finally removed the manifolds and filed them "flat" (very large file). But "flat" isn't the correct term, I actually filed them until all the port surfaces were on the same plane. I can take some pics if you like. I'm a machinist so if you do it incorrectly you'll make it worse. Anyway the stock manifolds (especially the centers) have thin ears which will bend over time with the heat and torque from the bolts. The tighter you torque them the more they bend making the problem worse. A few months after I filed them down they started leaking again. The real problem is that you don't know how many times other previous owners have machined or filed the manifolds...eventually they get so thin that it makes it really hard to get a good seal.
I finally went with the truck 360 magnum manifold on the passenger's side (they are super heavy duty) and 340 driver's side (which is also thicker than the original 318 manifold. Unfortunately I had to put 302 casting on the engine because the magnum manifolds have humungous ports. The large ports are great for power but won't seal good against the stock 318 heads.
In the pics you can see the 318 gasket in "blue" and in the second pic you can see how the 360 gasket swallows the 318.
Also pic of the extra 360 manifold I still have.
Good luck. I can post pics of my old manifold if you want a visual on the problem.
treblig in Tex
