I have been able to figure out a little more what is going on though.
The websphere app runs on a box that still has 7.2. It is hitting a database on a remote server that is 8.1, but with the 7.2 jdbc driver.
This is truncating the field names in the result set down to 29 characters.
I have a java program that does nothing but query a table for 1 row and then print out the field names from the metadata object, and can run it locally on the 8.1 server and get the full field names, and then run it on the 7.2 box/driver and see the truncation.
My solution should be then to just point to the 8.1 driver from within the websphere config.