This case (one machine with one license server system and multiple license files) should work fine and we support it.
In this scenario, one lmgrd process runs on the server machine and serves one or more vendor daemons, each with one or more license files; the license files usually are in the
From the documentation, to start the license server system just invoke the license server manager once on the server machine
lmgrd -c common_license_directory
lmgrd processes all files with the .lic extension in common_license_directory and
starts all vendor daemons referred to in those files, so there is no need to
enumerate each license file name on the lmgrd command line.
Also note, that it is possible to combine multiple license files by performing these steps:
1. Concateneate the files
2. Remove the duplicate SERVER and VENDOR lines.
For more details refer to 4.3 Combining Multiple License Files topic in the Using the IntelLicense Manager for FLEXlm* users guide (software.intel.com/file/6389)
If the customer still has this problem I would suggest to submit a ticket using Intel Premier Support or create a separate thread for SUS team using Download, Registration and Licensing forum.