That's really odd... So, to be clear:
1. MC12 on Machine 1 imported the files just fine. One question, was this the machine directly connected to the external drive, or the network machine?
2. MC12 on Machine 2 imported most of the files fine, but a selection of them didn't import tag data (so they have no Artist/Album/etc tags associated).
Is this correct?
I'd guess that the problem has something to do with accessing the big lossless files over the network. I agree with Jim as well, if the two machines have different versions of Quicktime, it could make them work a bit differently (MC uses Quicktime to decode the ALAC files). It wouldn't be the stupid character length restriction because they worked on the one machine and not the other. However, a few things...
The files on Machine 2 should all be accessible easily, even though they have missing tag data, in MC. They will simply show up under "Unknown" in the Genre/Artist/Album panes. I wouldn't do it this way though...
If you have the external drive mounted as a Network Drive, and it is mounted to the same drive letter on the network machine as it is on the local machine (in other words, if the "drive" is called "Drive M" to both machines) then you don't really NEED to import the files on both copies of MC. Simply import them on the local machine (which would be faster) and then use the same library on both machines. MC stores it's library files by default at: C:\Documents and Settings\<username>\Application Data\J River\Media Center 12\Library.
You can move the library wherever you want though by making a new one using the File --> Library --> Library Manager tool. I share my libraries between multiple machines. There are a few options for this, but the easiest one would be to just put the library ON the USB drive and point both copies of MC there. To do this...
You'll definitely want to have the drive "named" the same thing on both machines. I use Drive M (for "media"). So, assuming the USB drive is called Drive M on both machines, then make a folder called: M:\library_data\. Then, on the machine that "worked" (probably the one connected directly to the USB drive) copy the contents of the current library folder (probably the default folder listed above) into this new folder. Then go into the Library Manager and add a new library. You can call the library whatever you want (maybe "Shared Library") and then browse and select this new "library_data" folder. Load the new library and everything should match the way it was before with the default library.
Then close MC and go over to the other machine (the network one) and go into the Library Manager and repeat the procedure (not copying the files, just creating the new "library" in MC). Then both machines should match exactly.
The way MC works when two (or more) copies of the program on different machines point at the same library files is that whichever copy of MC "opens" the library first, "locks" them. Other copies of MC can open the library and use it, but they are "read only" which means you can't make changes to tags, or import new files, but you can use it to play files and whatnot. To get Read/Write access, you need to close MC on the machine that has it locked, and then restart MC on the "read only" machine. It works pretty well! It does this "locking/read-only" thing because if both machines had read/write access at once, the database would get all messed up.