Yes there is an issue right now when you do a run/run configurations that will overwrite that setting. To work around it, you can do the run from the toolbar icon in Eclipse instead or the command line.
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We don't use the command line. We experienced this problem on RhoStudio Eclipse implementation.
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There is an icon on the Eclipse toolbar that lets you do the Run instead of going through the menu Run/RunConfigurations. If you choose the toolbar run icon, you should not see the problem.
I had trouble finding this at first as well.
First time through, run as... configuration from the right-click menu on the project. Setup and save a new configuration. Give it a label and run it. It will overwrite the rhoconfig.txt.
Now go back and fix rhoconfig.txt. Do NOT use run as from the menu (every time you do this it overwrites rhoconfig.txt). From now on use the button in the Eclipse toolbar for run. Select the config you setup in the prior step from the pulldown & your app settings in rhoconfig.txt will remain intact.
BTW, I find git (and the SmartGit gui) very helpful for restoring rhoconfig.txt any time I need to create a different run configuration.
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Are you running using the toolbar icon or through Run configurations?