I too have SOME global variables now, "Optimized away", in C, using AStudio 6.1.2674, SP1, JTAGICE3, on ATXMega256A3U. Again, only some global structs have this issue, so I'm examining diffs in the data structures themselves, like, size, embedded pointers, structs, unions, anonymous or otherwise, and such. I too don't believe this is an optimization problem, I'm thinking it's a problem in the debug symbol chain?
Has anyone made any headway on this (besides rolling back to a previous version)?
//*** UPDATE ***//
Atmel Studio 6.1, SP2 seems to fix the "Optimized Away" problem, and updates the JTAGICE3 firmware. I've now safely rolled back to the future!