I've been running a series of tests with the same imagery (multiple conversion-to-jpeg parameters) and in one case, the correlation matrix disappeared in the chunks that were copied (via script) from the initial alignment chunk. I can't see anything different from the other projects - the alignment and optimization and script are all run in batch - (1) align, (2) optimize, (3) run script.
The script copies the original chunk and runs gradual selection, saving a new chunk each time it optimizes to a threshold value for first Reconstruction Uncertainty, then Projection accuracy, then Reprojection Error. All of the copied chunks have the correlation matrix grayed out.
I just tried copying manually and the correlation matrix survives the copy. I'll try running just the script again, guessing it will work, but wondering what would cause this...