Hmm - maybe another issue there. Do you think in the cases where it doesn't work the first time, MarsEdit is not running yet? That could be an issue I need to look into.
Actually, it happens occasionally when MarsEdit is already running. I'm not 100% sure if it's happened when the bookmarklet is launching the app. I use the bookmarklet a lot, so I'll pay close attention and report back.
Thanks. I may not be able to get this fixed for the 3.5.6 release, which I'm wrapping up now, but I'll make it a priority for the next update and try to get you a 3.5.7 beta to try ASAP.
You'll want to make sure the other copies of MarsEdit are thrown out so there is no confusion to the system about which version opens when you click the bookmarklet.