I originally had some apps installed on my SD card, and it worked fine... then I wanted to install Linux, so I moved a couple apps to a USB stick, and that worked too. However the Linux installer partitions the SD card, and HBC seems to have issues with that. When I start it up, the apps on the SD card won't appear at all, but if I start Homebrew Browser (from USB) and quit, all the apps show up again.
Additionally I had an SD card go bad, and whenever it was inserted, HBC wouldn't show any apps at all. As soon as I removed the card, apps on the USB stick would appear. It seems like HBC locks or gives up trying to read the SD card, and then just stops there instead of moving on to USB devices?