Can you please tell us if you see the same error for all applications that have reference tables ?
Also, when performing the import from Developer Client, please do check if there are any entries in INFA_CLIENT_HOME/clients/DeveloperClient/workspace/.metadata/.log file.
As you mentioned that some of the RTM files are of size 0kb. Could you please confirm if there were no issue while performing the export operation or are these files does not have any data in the source itself?
Please check in the env from where you have taken the export. If the reference file has data there, could you please try to export the application again and then import in the target.
You can also use developer tool for import and export if you have it installed on your machine.
This is working fine post updating the temporary file location in CSM configuration.