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If you are using a Real-Time operating system on the controller, then the modules will usually not be shown in MAX (CAN ports will generally show after the drivers have been loaded). Can you open a project and find the device and the modules? I am guessing that the error you are seeing may be related to the COM or USB ports as those are not shown. Typically in these scenarios I recommend the following troubleshooting steps:
Power down the device
Re-seat all modules (disconnect any external interfaces for troubleshooting)
Reset MAX configuration (Tools»Reset Configuration Data)
Turn the device on and reformat and reinstall the drivers/software (perhaps selecting all the install options for troubleshooting to ensure that you are not missing any drivers)
