Edit: above problem is caused by java updates being 64-bit. Re-installing the 32-bit java last fixes the problem. Symptoms are changed locations for both the settings folder and download folder, and error window when opening LW and disability of connecting.

That seems odd.

C:\Users\*MyName*\AppData\Roaming\Limewire is the default for Vista and Windows 7 for LW's preferences folder. Only reason it might be sent somewhere else is if a props file within the LW application folder is telling it to.

Which version of LimeWire are you using? Maybe a very old LW 4 version? I cannot remember which version of LW 4 changed location for the prefs folder, around 4.10 or so.
It sounds more like you are using a portable version of LW or something.

If you are using Linux then yes I could understand the file being in a location similar to what you described. I think C:\Users\*MyName*\.limewire is the default location for Linux, they still use the .limewire location.

I am sorry I have not created a similar installer for Linux. I tried a year ago and totally wiped an entire 1 TB drive, so I was not enthusiastic to try again after that though I did try at least. I do not use Linux myself.
I could create one to be installed via Windows, but do all Linux users have Windows installed on their systems?