How to set percent discount by old and new price
There isn't really enough information here to diagnose your issue, but the likely problem is a mismatch between the data type required by your custom field and the data type of your calculated value. Since you didn't specify the type of field you used to create your custom field, I can't say for certain, but Rules will only allow you to set it to a valid value for the field type.

At the very least, it doesn't appear to be anything to do with Commerce or Rules themselves.