You can try a few things to potentially solve this problem.
1. If you are not using a select series 2 version 08.11.07.536 or higher you may have encountered a defect attributed to having two(2) GPK files in the COGO directory.
2. The GEOPAKCOM did not register properly on your machine. So you can go to the BIN folder where you installed the software and as the administrator of your machine you can execute the file 'geopakcom.exe' This should register the geopakcom and you may be able to run now.
3. You could also try the following but you do need to have full control set in your user privleges
(1.) Close all DGN files
(2.) Bring up the dos prompt and change directory ("cd") to the following location (may be slightly different on your computer):
cd C:\Program Files (x86)\Common Files\Bentley Shared\GEOPAK\
(3.) Key-In "REGSVR32 BentleyControls.ocx" and press Enter.
You should get a message "DllRegistryServer in BentleyControls.ocx succeeded"
(4.) Now exit the dos prompt, go back into your DGN file and try again