This is one of the trickiest parts of shaft work IMO. different materials act in different ways. As hadj mentioned the expansion and contraction of materials can cause things to move after you have them perfect. You can do a shaft with a perfect seam , and within hours you might still feel a place Anyway. how I go about It sometimes depends on the material and My past experience with It. Sometimes It's as simple as taking longer, and letting the material cool from the friction, but that can be tough when finishing off due to any burmishing procedures. They only create more problems due to the heat buildup. sometimes you get the opposite effect, and the seam will feel off, but once It cools then It's perfect. Over time you get to know the different materials Your working with, and develope little tricks to make things easier the first time. It's easy to dig yourself a hole when learning, so you have to be carefull or could end up in a real mess trying to fix It. but IMO hands on is the best teacher in this area. Possible what I do May not work well in another area with a different climate & humidity level.
indicating and shimming can also help, as well as centering drilling for a live center as It's helps cut down on the pushoff from your cutting tool. Just make sure as mentioned that the shaft part is indicated, because sometimes a center hole that's not perfect can throw that off, and defeat half of the purpose for doing it. As mentioned Keeping the ferrule closer to the headstock can help with some issues also, and may be easier to indicate. You can even undercut the ferrule slightly, and sand the wood to the ferule, but may loose more diameter that way depending on equipment or how close you can cut it.
As Sheldon mentioned the most damage in this area is usually caused from excessive customer sanding or those green scrubby pads. some can be very hard to work with, and as he mentioned many times they are also out of round making the indicating alittle harder, and the repair guy having to resort to stuff He'd probably rather not have to get into.
Besides expasion issues, The best way to explain why you have some that blend easier and others that are a pain, might be because the wood and most ferrule materials sand at a different rate, and the wood most times sands away alot faster making that seam even worse the more you try to blend It, as where some materials sand alittle closer to the same rate as the wood, but keep this in mind, some shaftwoods sand away faster then other shaftswoods LOL. Brings up the forest theory, "It's like a box of chocolates".
I've been through many methods of sanding, some decent and other just made things worse. The board sanding I've done before, It helps to keep you from pinching with your fingers as mentioned, and making the area in ? even worse, but I only use It on rare ocassion now. The method of sanding I use is simular to the way you sand the finish on the cue, and I try to never put Myself in a position where I need anything under 400 grit. I'm all about taking off as little as possible to get the job done, as I'm sure most others are.
I hesitate to mention this because I don't avocate it, some may frown on It, and others may try it only to have poor results and more headaches to contend with, but sometimes good ol CA can help in this area also. I don't mean for filling purposes, but just to seal the seam and slow down the sanding rate of the shaft wood some. It is very hard to apply & do perfectly, and took me quite some time to perfect, so I don't recomend it, and in fact only do so Myself when it seems all else will fail. You can make a real mess of things, and there are many other issues that can be brought on by it. Not something you want to experiement on a customer cue with. Also If not done corectly or filling with it too much, can make It noticable when the shaft is polished. I have customers that like different types of finishes, and I do have some that like more of the chalky, sanded, smooth type finish, so are more concerned with keeping what ever diameter they can. With that type finish the CA blends well and helps keep some diameter to their shaft, so they are very happy with the results even as a filler. Now when you are doing a super burnished shaft you need to be on the money the first time, and try to avoid it all together, but It is possible to apply and sand just through it enough so It does'nt stand out or cause a difference in feel where you used It.
Keep in mind this is not what I consider regular practice, but I do have customers that will just sand their shafts down to nothing, so these are the ones I am refering to. If you don't result to giving them something to sand on there, and just cut the ferrule down each time, before long they will be shooting with a pencil. It simply buys them time before they have to replace the shaft, and they are fully aware of why I do this for them.
Assuming that Your centering when cutting is not the issue, but you are moreless striving to have a perfect finished seam, I would add this, Try to think of sanding as if your finishing a cue & that may help some. The lathe does'nt always have to be spinning when you do it, the art of it is in the hands, mind, and how they comunicate & work together. I know that sounds corny, but what I'm saying is an artist can give you the tools, and can even explain the strokes to you, but he still can't make you paint like him. somethings will just come to you in time, and as long as your trying to strive for perfection and are persistent, then you will be seeing the results You desire. I'm sure you've had time to figure out that part out already, and are probably like me and just want that area perfect everytime. Some can still be a pain no matter how many tricks I learn. The main thing I've learned is not to cause yourself anymore work then possible, because in the end you will be less satisfied with the results anyway. I have pretty good luck with them now, but every once in a while I get one that has me pulling My grey hair & Ca out
Good Luck, Greg