EMA isn't perfect, but it does work. It's going to need time to get through the trade losses. I honestly don't suggest letting it dabble with mtgox right now. The market is simply too volatile right now, especially mtgox. I shut off my mtgox trader, but have made profit with btce the past few days. Yes, I have made BTC with btce this past weekend.
I don't suppose you'd share your settings for BTCE over the past few days? I've lost on the last few trades - I'm not complaining, I understand the long term concept and I've read up on EMA etc. but it seems there are a lot of opportunities I could have taken advantage of with some better settings over the last week. Even moving down to 15 mins would have put me in a better position, but everything I've read drums in the idea of not going below 30 mins. Having said that, moving up to 2 hours would mean I'd still be long from about $300 which might actually be preferable!
The EMA numbers seem pretty arbitrary, I can play around with them and get better results in back testing, but I can't predict what's going to happen to the market so I'm generally sticking to safe numbers.
Goomboo's thread gives some nice info on what EMA is and about sticking to the system, but I can't find much info on deciding on your settings.
Since July 2013 when I started using this Bot, I have lost on probably 70% to 80% of my tades it has made for me.. But they have been small loses(% wise)..