If you look under the PCN (Product Change Notifications), you will find documents that describe each hardware change, including CPLD code that we make.
http://www.logicpd.com/auth/downloads/LH7A404/#changes
You will find two docs, one for CPLD code 3.1 and one for 3.2 that discuss what has changed in each.
PCN 285 LH7A404-11 CPLD Change v3.1
PCN 287 LH7A404-11 CPLD Change v3.2
I believe the changes documented in PCN 287 are likely your culprit here.
Thanks,
-Mike