I've investigated this and it looks like the combined Hero Clix data files are running up against an internal limit in Card Vault has, which is causing the "out of memory" message. If you delete a few of the .dat files in the new combined folder you can fix this, but then you won't have access to the content in those files.
I'm afraid I don't have any good answers for you on this, as I'm not sure if we'll be able to fix the issue. I've removed the suggestion on how to merge DC/Marvel Heroclix from our web site, as it no longer applies given the volume of data present.
Sorry for the bad news - please let me know if you have any further questions.