Hi Todd,
I wasn't able to reproduce this using mongoimport v2.2:
> mongoimport --port 30001 -d test -c comma --file test.js
Tue Oct 23 12:30:16 imported 1 objects
> cat test.js
{ a: "a,b,c,d,e", b: "f,g,h,i,j" }
> mongo --port 30001
MongoDB shell version: 2.2.0
> db.comma.find()
{ "_id" : ObjectId("5086c6187f9c0acd2a40cb14"), "a" : "a,b,c,d,e", "b" : "f,g,h,i,j" }
What version of mongoimport are you using?
-Stephen