Rogan,
What kind of interleaving paper are you using? A smooth paper will have less tendency to pick up ink from your print, but what you describe is a property of the MK (matte black) inks used in the Epson 3800.
At the same time, matte papers generally don't do too well when you try to use PK (glossy black) inks on them.
In my tests of matte papers, I have not found one that is totally free of transfer from the surface of MK black ink. They all do it if given enough opportunity for abrasion against other paper surfaces, especially ones with some "tooth" to the surface. PK inks do not come off in this way. Moab Entrada 190 didn't do too badly in my tests, compared to some other matte papers, but it reaches it's maximum black somewhat early on (around 60% black ink), and then more black ink just increases the likelihood of transfer but does not improve dMax. In fact, there is a slight reversal in the measured reflection density as you go above about 75% black ink.
A double-sided matte print portfolio, or even a single-sided one should have a smooth acid-free interleaving paper between pages. If transfer occurs, the interleaf paper can be changed, and usually the transfer does not show up as smearing on the print itself.
For maximum durability, though, as in a book, use papers that take the PK (glossy black) inks (again with a non-abrasive interleaf paper). None of the papers I've tested that use this ink show a tendency to transfer the black ink, though some have a somewhat fragile surface. If you like the white surface of the Entrada, you might try Epson Exhibition Fiber. It seems pretty tough, but it's not double-sided like the Entrada. It and the Hahnemuhle Photo Rag paper (the new one that has no OBA'a) give virtually identical ink curves with very high dMax numbers, but with different surface appearances.
Now, here's the good news: If you prefer the look of the matte surface, you might try using a spray protective coating of a type that leaves the surface appearance unaffected. Use three light coats. This may eliminate the transfer problem. Test it first to make sure it's compatible with the paper you are using.
Aloha,
Aaron