To clear somethings up I did some more testing with a booster from @scottmcl. I found out what is actually happening is that when an effect occurs within the first second of the song it sometimes is skipped. If the first note gets skipped it immediately starts correctly with the second note. I tested this having Xlights output the signal from my laptop and from the master Pi and both had this skipping issue.
Is this a known issue to anyone? Can it be fixed if you add 1 second of nothing at the start? I did find out that the standard, high speed and booster RS485 adaptors all work the same with my setup.
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