Don't worry - there's nothing broken. The Spooky2 Remote LEDs respond to and mirror exactly the shape of the waveform you're transmitting. Normally, all waveforms have two phases - a positive one, and a negative one. If you look at any wave, you'll see that it rises, and it falls. When it's rising, it's going positive, and when it's falling, it's going negative. During the positive-going phase, only the left LED lights, and during the negative-going phase, only the right one illuminates.
If you examine the shape of either of the sawtooth waveforms, you'll find that one of its phases is a long slow rise or fall, while the other is an almost instantaneous rise or drop. Since the LEDs reflect the shape of the waveform, the result is that one of them will appear to be dimmer than the other any time you're using a sawtooth waveform.
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How Does Spooky Remote Light