I have finally found the bug regarding BTC-e monitoring. Gekko broke over BTC-e monitoring because bitcoinCharts (the API Gekko uses to get trade data from BTC-e) changed the way services can ask for trade data (silently).

Current workaround for BTC-e users:

• Set debug in the config to true (line 145)
• Set the candles to something lower than 40 (line 22)
• Run Gekko
• Check whether the calulcated EMAs are NaN, if they are lower the 40 number

The reason the 40 number can be different is that now bitcoinCharts will return the last 2000 trades, and how long ago the oldest one happened depends on the market.