Normally, pitch macro values act as relative values (each value is added/subtracted from the previous value). However, when you use an arpeggio macro, pitch values act as absolute values (each value is added/subtracted from zero) until the arpeggio macro ends (unless it's looped). Observing the instruments in the FTM below should give you a better idea of what I mean.
I believe it's intentional. I can't remember why but it had something to do with the calculation of the pitch. It's also why pitch bends don't work when you use an instrument with an arpeggio macro. You probably should ask Slimeball or rainwarrior about this.
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This happens because the arpeggio macro is overwriting the pitch value for each new note, which resets the previous pitch macro values.
It is sort of intentional, but would probably be possible to "fix" by storing the accumulated pitch values separately. I'm unsure if that would be useful though, other than making it a bit more intuitive.