Okay, I think it is pretty much ready.
http://www.mediafire.com/download/72alq0y77xf2gkf/TWRP_multirom_grouper_20130919.img
http://www.mediafire.com/download/h44bcjq059qqq4n/multirom-20130919-v13-grouper.zip
Version 13 doesn't really bring many new features, but it is using the "shared codebase", meaning the code works on multiple devices, meaning version for flo is nearly ready. If it goes well on grouper, I'm aiming for release early next week.
In the meantime, I would like you to use and test MultiROM as much as you can - a lot of code has changed and bugs might have crept in and we certainly don't want them to live on. But, I've also implemented backups for secondary ROMs. The ROMs must _not_ share the kernel with internal though - I simply don't have enough data to create full backup image without that. Also,
Don't share kernel is now default option when adding ROM.
As a part of my testing of v13, I've installed Ubuntu several times, but I can't reproduce this. Did you have enough space in /data? I know that some old versions of CM refused to boot if there wasn't enough free space (i.e. when the "Not enough free space" notification would pop up in Android), I don't know if that's still the case. Did it happen immediatelly after installing, without first boot to Ubuntu? All the logs you can get are welcome.