What type of JLink application are you running, Sync or Async? If you are running a Async then you need to review your environment variables. The example of the paths are shown below.
path = (ProE LoadPoint)\i486_nt\lib\
PRO_COMM_MSG_EXE = (ProE LoadPoint)\i486_nt\obj\pro_comm_msg.exe
And make sure that the pfcasync.jar file is listed in the path statement. It is best to set these environment variables in the start Pro/E bat file.
Now for a Sync App:
Check to the see if the protk.dat file is register and make sure all the paths in the protk.dat file is valid for the user.
If you have any questions or concerns you can reach me at email@example.com
Hope this helps.