I've done exactly this, and have "minimize tool changes" checked, but it still orders them by setup, not by tool.
My setup:
I have a carrier board positioned at the origin of the machine, G54. The carrier has a one-inch grid of mounting holes and on it are three pieces of stock at different positions. One on piece of stock I machine a pattern of 3x3 parts, on the next a pattern of 7x4 parts, etc...
So I have three setups in CAM. Each uses G54, the position of the carrier, each defines the stock as the size of the carrier board but uses offset to position the actual stock where the pattern should start on the board. Each pattern has three operations: a pocket, drilling, and a profile.
When I select the three setups and post, I get the warning about multiple WCS, I check "minimize tool changes", but the post is just each setup in order rather than T1 setup1, setup 2, setup 3; T2 setup1, setup2, setup3 .. etc
Is there anything else I should be doing? I have to go edit the file by hand to cut and paste the blocks of code into tool groups...