FYI, AutoBeanCodex.decode uses StringQuoter, whose super-source implementation (used in compiled code only) uses JsonUtils.safeEval, which in turn uses eval() in IE6 to "parse" the JSON, after checking it with a couple regexps. So maybe the regexps are slow with large strings?
You could try overriding the StringQuoter (put your version earlier on the classpath) with a version that uses JsonUtils.unsafeEval to see if it makes a difference (at your own risks).
But AutoBeans do create a lot of objects (an AutoBean and a "wrapper" implementing your interface for each object in the JSON), and that could really be the bottleneck in your case.