Matt,
Please double check your gel file and also board init call for custom board.
Kindly have a look at the below wiki page for AM1808.
http://processors.wiki.ti.com/index.php/EVM_Overview_-_AM1808
http://processors.wiki.ti.com/index.php/How_to_connect_to_the_OMAP-L138/C6748/AM1808_EVM_board_using_CCS%3F
This wiki page gives the detail of AM1808 and LogicPD example code link.
I can suggest you, take the timer code as a reference from LogicPD for your own custom board(AM1808), if possible to you.
(Please visit the site to view this file)