I suspect that you're getting some low frequency noise coupling, maybe from AC line pickup or a switching power supply, etc. You have your trigger level set pretty high on the waveform, so it's likely only going to pickup the momentary peaks when this interference occurs. If you adjust the trigger point down, I'd bet that you don't see this because it will be very infrequent compared to your 1MHz input signal. Can the scope tell you the Trigger frequency? That might give you a clue too.