I am not sure what is causing your problems, you have gotten really good advice here too. I do not normally export to mp3 but use flac and sometimes wav and have processed some large files and never had my Babyface act up in that scenario, or any situation for that matter.
It is possible you have a defective unit.
BTW:
I swear by RME having used their gear for over 5 years without issue, I now own three RME audio interfaces:
I have an RME HDSP 9632 at home with Sonar Platinum and Win 7 Pro on an i7 desktop with 18Gb of ram.
On the road I use a Babyface with my Laptop, a decent Lenovo with an Intel i5 and 8G of ram running Windows 7 Pro and Sonar X3e. Never had a problem with the BF on the road <close to a year of road time by now>.
This last trip I forgot my BF so I picked up the Babyface Pro.
Wow! what a difference, the Pro is incredible, it just seems to have more 'guts' is even cleaner, if that is possible and seems to have more headroom. Now that I am back home I want to try the BF Pro on my home machine in place of the HDSP 9632. Perhaps I will keep using the BF Pro at home too!
Check with RME and let us know how you make out. Cheers, Dave