thanks for the replies. Its tempting to not trust the Cheshire
I will give it another shot over the weekend. But just wanted to confirm that cheshire will be the right tool to use to centre and align the secondary.
For what it's worth--the collimation cap and a Cheshire eyepiece are both primary mirror alignment tools and both should show the same alignment. For the collimation cap, the corrected primary mirror tilt alignment will show the primary mirror center marker/donut surrounding and concentric with the collimation cap pupil. For a Cheshire eyepiece the primary mirror center marker/donut will be centered and concentric with the bright Cheshire ring. Both tools magnify any residual primary mirror tilt error 2X. This crititcal alignment centers the "sweet spot" in the eyepiece field of view.
The part of your "Cheshire" that doesn't seem to agree with your collimation cap is the sight tube portion of your Cheshire/sight tube combination tool. The sight tube cross hairs show you where the focuser is pointing (adjusted using the secondary mirror tilt screws), and the bottom edge of the sight tube shows your secondary mirror placement (adjusted by rotating or moving the secondary mirror closer to or farther from the primary mirror end of the tube assembly). These two connected alignments are separate from the primary mirror tilt alignment, and should be completed before making the final primary mirror tilt adjustment.
The cross hair alignment to the the primary mirror center marker/donut delivers optimal focus ensuring the primary mirror focal plane will be perpendicular to the focuser/eyepiece axis. Together with the primary mirror tilt adjustment, these two alignments deliver image performance and "snap" focus.
Getting the secondary mirror correctly centered under the focuser delivers centered and balanced field illumination in the eyepiece. Of the three alignments, this one has the least impact on image performance. Unfortunately, many beginners will adjust their secondary mirror so they can see all of the primary mirror clips at the expense of the more important cross hair alignment. The visibility of the primary mirror clips by itself (without a correct cross hair alignment) is NOT a valid indicator of good alignment!
Getting the secondary mirror correctly centered involves the alignment of three circles: the bottom edge of the sight tube, the actual edge of the secondary mirror, and the reflected edge of the primary mirror. When all three circles are concentric, the secondary mirror placement will be correct and the cross hair alignment will also be correct (or very close).
If your sight tube is too long (or if it can't be inserted deep enough into the focuser drawtube/2- to 1.25-inch adapter), you may not be able to see all three circles. At f/6, as long as you can see the actual edge of the secondary mirror (it helps to boost the visibility of the secondary mirror edge if you put a sheet of white paper behind the secondary mirror against the inside edge of the tube wall opposite the focuser) and the cross hair alignment, you should be able to get your collimation sorted out.
Use this diagram for reference: the outermost light blue circle is the bottom edge of the sight tube and blue cross hairs are the sight tube cross hairs, the green circle is the actual edge of the secondary mirror, the red circle is the reflected edge of the primary mirror, the yellow circle is the outer edge of the bright Cheshire ring, the small circle in the middle is the primary mirror center marker/donut, and the black dot in the center is the Cheshire pupil (the violet circle surrounding the bright Cheshire ring is the silhouette reflection of the secondary mirror, which appears offset toward the primary mirror end of the tube assembly--ALL of the other circles are concentric). Also note that the spider vanes will probably not coincide with the sight tube cross hairs--so don't use them as an alignment reference!