I finally got iSeriesAccess to run on Ubuntu. The problem was staring me in the face. The error message I kept getting was:
5250: [ INFORMATIONAL ]: Build Date: 13 July 2005 (1.10).
*** glibc detected *** free(): invalid next size (fast): 0x0838ff80 ***
The fix (maybe a better way) was simply starting it up like this:
./ibm5250 -LANGID en_us