Perhaps this is a limitation of 0.9.3. I can open Eye TV files just fine with a recent SVN of HB. Hopefully dynaflash or eddyg will chime in here.
probably a side effect of removing the ads. Try it on a test sample from eyetv without removing the ads first. Note that unreleased versions of HB are better at this than 0.9.3 - however it should still work.