OK, let's forget about the start command for a bit. (Maybe Dias has an idea why the /B is being ignored.)
I think we are going to need a lot more details, if there is any hope for a batch file resolution to your problem.
Fluent & Matlab must be DOS programs, Right?
Are you running Fluent & Matlab in Windows XP in a CMD window, or in some other version of Windows or DOS?
I take it that you can get the results you want, if you run the commands from the CMD window, in the proper sequence, and that now you want to automate the process with a batch file. Right?
Can you explain exactly what commands you are using at the command line and the procedure for inputting the data from the results file that works for you(from the command line).
Also what do you mean by this:
My goal is to have MATLAB give an initial set of conditions to FLUENT, trough a file it writes and that is loaded as the journal, and after FLUENT reads the file and executes the commands, it creates another file, that is "fed" into MATLAB, and they keep doing this in sequence for an x number of times.
What is the purpose of "feeding" the data from one program to the other repeatedly, as you describe?
I hate to say it, but this all sounds very complicated, and may be very difficult to accomplish, especially, considering the fact that the Matlab forum guys are stuck also.
I've seen in a matlab forum that maybe tracking the matlab session id, but neither they nor I have any idea how this can be done!
Explain everything you do at the command line in extreme detail, & maybe .....
Also, how about a link to the matlab forum discussing this problem.