Ok....confirmed. I uninstalled BI5 (actually did full windows install again just in case) and then installed. I tried the auto-cycle from the install (installed version from my cd was 5.0.0.57) and it worked great. It only auto-cycled though the cameras in the specific groups. The only way to auto-cycle through all 9 of my cameras was to select "All Cameras" drop-down in the upper right of the screen. THIS is what I think is accepted, normal behavior. I then let it do an update to 5.0.6.4 and it would not auto-cycle to only the specific group.
To "fix things", I uninstalled the software (rebooted just in case) and then installed again off the cd (which set met to v5.0.0.57) and disabled any sort of auto-update.
Lesson learned was:
1. use Settings>Export Settings to save your settings before changing or updating. If anything borks, you can uninstall, then install from the cd again, import your settings quickly & easily.
2. disable Settings>Software Support & Maintenance>prompt at startup, re-check, & Automatic download and install. Whenever I want to do an update, I'll export my settings first in case I want to go back to the cd install.
I'm sure the creator of BI is doing a great job, the auto-cycle is just kind of broken as of 5.0.6.0 & still broken as of 5.0.6.4. I'm confident he'll get it fixed eventually. I just wanted to let people know as of what I'm seeing now & how to mitigate it.