Looking more narrowly - the question was why do you have problems with the Ubuntu system, and it seems there is a known bug that gets triggered when you mount UFS filesystem. So the solution is to not do that and see whether any other problems arise.
As for copying files, if you are doing developement it can be helpful to have one stable system using, for example, Ubuntu and ext4 that hosts the files and you copy them back and force over network using NFS for Linux and BSD and samba for Windows. 10Gb adapters (and switches) are pretty cheap nowadays.