I know this is an old thread, but I recently had this issue on an Ubuntu laptop and found that my preferences.txt indeed had a baud rate other than 9600. From my reading (I can't find the link now) I found that this is due to the bootloader's baud rate. Some versions of the bootloader use a baud rate other than 9600. That is the reason for the IDE installing with an odd baud rate.
The reason that running the IDE as an administrator works is because on linux, even if your user is part of the dialout group, the user is not allowed to change the port settings. However, the IDE will try to change the baud to another rate when it knows that the boot loader requires it. As an admin (sudo) you are able to change the port, but not otherwise.
Thus, I changed the baud rate in my preferences.txt and all is well. No need for sudo.