Mark,
I use custom "measure" charts for reading CCs or a small set of colors I want to record but always use spot mode. I haven't encountered any issue in that mode. For I1Pro2/i1iSis charts, even when not making profiles, I use the profile making path out of convenience and just save the data after measuring the chart. I have never tried the custom path in other than spot reading mode. Am I not encountering it by accident? What is the nature of the bug?
I am also measuring in Spot Mode.
(1) Let us say in Measure Chart you have defined a custom chart with 1 row, 30 columns and saved it as a workflow. It's one row of 30 patches.
(2) When you want to use that workflow, you open Measure Chart, click on that workflow, and in the Measurement tab you will see a chart of 506 patches, not 30 patches.
(3) To correct this, you need to go back to the Define Chart tab and change the number of columns say to 29, then change it back to 30, and this will jog what appears on the Measurement tab to the correct 30 patches in a single row.
X-Rite is well aware of this problem, they've replicated it, but they are either too cheap or too lazy or both to put the resources into fixing it - a long time running.