On CCS6, I created a new .ccxml Target Configuration file from scratch for my F28069 board (custom).
Then I created a new Debug Configuration to use this new target config file.
When I launch the debugger with the new debug configuration, the XDS100v2 does not connect, and the program does not load. However, I can choose Run/Connect Target... manually, and then Run/Load/Load Program... manually, and the program will load and continue to the breakpoint at main(). My debug configuration has the Auto Run and Launch Options checkbox "Connect to the target on debugger startup" enabled. See image below.
I never used to have this problem with CCS 5.5.2.