First of all, I've never seen a system that uses % as reference operator, this is the $ sign. Check your system!
You have to use absolute references in your formulas too!
Switch between relative, absolute, and mixed references - Excel
If you use relative references, you must select the first of the applied range, otherwise the formula changes!
Example:
Select A2
Add a CF using this formula
=B1=""
Then apply to A1:A2
In the moment you apply the CF the formula changes to
=B1048576=""
This behavior is normal if you use relative references, there is no issue if you use absolute references.
If you need further help share your file.
Andreas.