I tested my theory of changing the initial RTC within the savestate file. It didn't work. It took a change of at least 1000 to yield a different initial seed at the beginning of room 2.
Further, that seed did not change equally to the change in RTC timer. For example:
Initial RTC Initial Seed
1000 34203
1500 34203
1999 34203
2000 55990
1000000000000 46218
According to c-squares lua script. The number of 'changes' when the initial is set varies drastically with different initial RTC values as well.
Any ideas?
EDIT: With further testing...
Starting RTC of 86400000 = Starting of 0
Starting RTC of 86401000 = Starting of 1000
So it seems that a change of at least 1 whole second in RTC value is necessary to change the initial seed....though that still doesn't explain why the initial seed changes at a different rate than the milliseconds after midnight.