I'm using bsnes-plus v05, the latest available here.
Taking a look on this image, you might notice the current opcode to be executed on the first panel shows sta $6303, y where y is 002c as you can see on the right. However the address on the right side that the disassembler shows is actually $63FF, which is $6303 + SCPU's Y register and not $6303 + SA1.Y register. S-CPU's Y register is set to $FC at this moment.
The third panel ('old' style disassembly) is not affected.
I'm using bsnes-plus v05, the latest available here.
Taking a look on this image, you might notice the current opcode to be executed on the first panel shows sta $6303, y where y is 002c as you can see on the right. However the address on the right side that the disassembler shows is actually $63FF, which is $6303 + SCPU's Y register and not $6303 + SA1.Y register. S-CPU's Y register is set to $FC at this moment.
The third panel ('old' style disassembly) is not affected.