Before I can offer any detailed suggestions, I'll need to ask if you're using PanoWeaver Pro for your pano stitching. The "Pro" version allows for manual alignment of your stitched image after the auto-stitch function has run. Manual Mode lets you do 2 things:
1). You can fine-tune how the images line up with each other and see the results instantly as you change the numbers.
2). It displays the alignment parameter (Y/P/R/FOV) values so you can write them down. As long as you use the same camera and rotator for each future pano you stitch, these values should work fairly well.
There's a settings window in PanoWeaver Pro you can access by clicking:
Tools > Auto Stitching Parameter Settings
Within this window you can enter the "degree ranges" for each axis that PanoWeaver will work within in determining the optimum alignment of your fisheye images. Typically I'll set them to be around 1 degree each way of my "optimal settings", based on a test image. In other words, after Manual Mode alignment on a difficult image with a lot of geometry (like a tile bathroom!) I'll write down those numbers. If the best Yaw angle turns out to be -0.4 degrees, I'll set the PanoWeaver Yaw Range from -1.4 to +0.6 (which is a 2 degree range, 1 degree both ways from -0.4).
As time goes on you can narrow this range down even more to save stitching time. But as you do, when you see a perfect stitch, go into Manual Mode and see how close those numbers are to your original range settings. Over time you'll get an "average" perfect range for your particular setup, and can refine & narrow your ranges from there.
IMPORTANT! What I've found in my experience is that it's a good practice to always start capturing your panoramas with the rotator in the same position. To explain, I once had an old IPIX rotator that click-locked at 180 degree intervals. After testing, I learned it was more like 178.8 degrees. So I placed a little stick-on dot at the base of the rotator (the non-moving part) so that I could make sure I always took the first fisheye shot from that click-lock position. Since you're using the 3-fisheye method, I'd suggest also making sure your rotation direction is always the same (clockwise or counter-clockwise.)
What this does is ensure that any geometric/mechanical tollerances in your rotator are repeatable and consistent with all panos you shoot. That will help enable you to fine-tune your stitching parameter angular ranges with your particular hardware rig.
Sorry to be so long-winded, but I do hope this helps you. It's amazing how many little "tweeky" things can affect an otherwise seamless pano.