Putting this up so its a known issue until I close it, or get some help from @Speiger ,
For some reason when using an Item Translocator to filter fluid tubes, it will convert all other tubes into whatever successfully gets transferred.

For example: Setting the filter to a Hydrogen filled Test Tube to filter the output of Bauxite Dust processing (Oxygen Tubes, Hydrogen Tubes, Aluminium, and Titanium Dust) the Translocator will successfully pull the Hydrogen tubes out of the machine, but in the process convert the remaining Oxygen Filled tubes to Hydrogen tubes allowing for duplication of ANY fluid container.

Don't really know why yet as I've tried to use .copy() in various places to maintain any possible lost NBT data for the container and it seems to have no effect. Cant tell if its in the filter or the transfer itself. Will continue to mess with this for the next release (1.1.2).

Nvm I Fixed it, @Speiger your BasicItemFilter(foo); does the lazy version of your StackUtil Compare method so it ignores nbt!