BYOND Portable writes to C:\Users\User\Documents\BYOND when executed for the first time. This is the default location where BYOND stores all user configuration information and "my hub" (game/library) downloads. The only easy way to change this location is by using BYOND.exe to change BYOND preferences.
Seems there was a change in the app and it won't create its own specified directory. You can fix this for a first run by creating a directory called BYONDData within the BYONDPortable\App\DefaultData directory. That will ensure that BYONDPortable\Data\BYONDData exists. I'll work on a revision to fix this issue.
Sometimes, the impossible can become possible, if you're awesome!
This is fixed in BYOND Portable 5.0 b511.1385 Rev 2. The installer will attempt to detect this situation, automatically copy them in, and notify you that you may delete the local settings if you don't use BYOND locally. Our apologies for the inconvenience.
Sometimes, the impossible can become possible, if you're awesome!