I believe the issue is a consequence of the way data is organized during experimentation and then determining how to best bring it into JMP.
In experimentation, you have multiple scans of the entire 2theta range at varying temperature. This would give a single data file of 2theta vs. intensity (what we have been discussing as 'x' and 'z' with an annotated temperature ('y') value. Doing multiple scans at multiple temperatures gives multiple data files of 2theta vs. intensity with annotated temperatures.
When I had access to matlab, as all the 2theta values are constant throughout all data files, I could write a script to strip the data from all data files with a matrix for 2theta [x1, ... , xn], a matrix for the annotated temperatures [y1, ... , yn], and a resultant matrix of the intensity values that correspond to each xi, yi.
That ficitonal data set was a representation of an attempt to pull in the original data for each scan (thus one 2theta column with multiple intensity columns) without the knowledge of how to incorporate the temperature data in the JMP data sheet format.
Another avenue would be to just use scan number as stand in for temperature as the scans are done continuously with regards to the changing temperature.