What version of the PI Analysis are you using?
Is there any TableLookup attributes in use with your SQC analysis? Are you testing this with the same element?
I would also recommend to create a techsupport case on this as configuration of your template and element may be required for further investigation on this.
Sorry for the very late reply, but I am now revisiting this again. Yes, the control limits are coming from table lookup values, and yes, it is being tested with the same attribute.