Actually, I misunderstood my problem. I have previously been using HEM's "copy hands to clipboard with stats" feature, which reformats the hands into a standardish format. Last night I was trying to use "copy hands to clipboard" which just leaves it in the site format, which is not supported. So the hand converter is fine. I was just trying to convert unsupported hands.
What site are you playing on? Sorry for the lack of response, didn't see the thread the first time around. As Unstable James posted, there are multiple formats that HEM copy/pastes to. If you can paste the HH in here we can take a look at it.