Hi, I'm not LV expert but I think I run into some thing like yours before. What I did was checking any missing pulse or abnormal in the EEG waveform and set trigger pulse once I found it. Take a look at your signal amplitude. If your signal too low (ex: <1.25V), your counter gate won't trigger. Once you record your EEG, amplified it and use trigger VI (take a look at the LV example) to set your trigger event pulse.
BC