Does anyone know why I'm getting an invalid reference key for a custom segment that is blank on the upload spreadsheet when doing a CSV import? The reference is an inactive custom segment but we want the custom segment to be blank and it's being forced to have a value

You probably have a hidden character in the cells - I'd make sure it's completely and truly empty with the excel function for Clean(cellreference) or by deleting the cells/copying properly blank ones over it

It is completely empty. Also a previous upload that went through also had a blank custom segment value but when it got uploaded, it was populated (the first value on the list - internal id =1). I looked at the Custom Segment set up, there is no default value

is there a workflow or script that is potentially populating that custom segment? and this is a csv import that creates a new transaction (as opposed to an update)? Perhaps using the "overwrite missing fields" option under the Advanced Options screen of the mapping assistant will help?