One thing I had to change before it worked for me was taking out the "" around 3DO and Jaguar. I would also check inside phoenix.config.xml to make sure that the paths for the games are correct. For some reason two of the Jaguar Games didn't show the correct path after I added them to database in Phoenix. For example I've got AVP in C:/LaunchBox/Emulators/Phoenix/Jaguar/CARTRIDGE/Alien vs Predator (World).j64 so in the config under the Jaguar Section which now shows up correctly as:
<Dump path="C:/LaunchBox/Emulators/Phoenix/Jaguar/CARTRIDGE/Alien vs Predator (World).j64" size="4194304" fast-md5="96bc77cfd1b2df85b5e6ae05594e74b0" md5="96bc77cfd1b2df85b5e6ae05594e74b0" sh1="fd8c89250ebc1e403838b2e589d1f69e3fe2fe02" />