Can I run a circadian rhythm sequence for different shifts?

Yes.

The only restriction of the system is that the controller can only run a circadian rhythm sequence at 3 different times in parallel.

If the system was to start the same 8 hour sequence in Room 1 at 9am, Room 2 at 9.30am, Room 3 at 10am, it cannot run another sequence until one of the other rooms finishes. This is an unlikely setup. More likely, the system would be running a midnight to 8am shift, 8am - 5pm, 5pm to midnight on all rooms starting at a certain time, which is fully catered for.

Generally speaking, the user may opt to only create a single circadian rhythm sequence that is reused at several times during the day but up to 3 different sequences can be created if variations are necessary.