Ok, noted the problem with the comments in sequence. The current pattern parser needs some reworking anyway, so I'll fix this problem when I get around to that. I'll think about the comma thing too, it'll require some extra code but can't hurt to make the parser more robust in this respect.
Since you were wondering, I'll try to give a better explanation of what the effect settings do.
The basic thing you have to understand is that the first two channels each use two semi-independant oscillators. Semi-independant because they share the same frequency divider ("A" resp. "B"). The output of the two oscillators is combined using the MIXA resp. MIXB method. This works the same way as in Shiru's Phaser engines (namely Phaser2/3, Phaser1 has only XOR mixing).
Before the mixing, a pre-scaler is applied to the first oscillator (PSCA1/PSCB1). This prescaler will shift output from the first osc up or down by one octave. After mixing, a post-scaler is applied to the combined output (PSCA2/PSCB2), which again shifts one octave up or down. This feature will probably be removed in favour of a second pre-scaler in the next version, because it's not really necessary (I was originally afraid that tone range would be insufficient, but that seems to be not the case).
On channel 1, there's also the duty modulator (DMOD), which should theoretically do what the "Duty Sweep" effect in HT2 ch2 does. However, the implementation is so slow that the effect is barely noticable - I'll probably replace it with something better in the next version as well.
Last but not least, there's the phase offset (PHA/PHB). The value you enter here is used to initialize the second oscillator before the sound loop (the first osc is always initialized to 0). If you don't use the pre-scaler and set MIXx=xor, this will essentially act as a duty setting (4xx/5xx/6xx in HT2). Setting PHx to $1000 will give a 50:50 square wave, $800 would give 25:75. There's no point in using values >$1000 unless you have PSCx2 set to "down" - in this case, $2000 will give 50:50 duty. Likewise, if PSCx2 is set to "up", $800 will be the max.
Channel 3 on the other hand has only one oscillator. PSCC is a post-scaler. Here, post-scaling makes sense because it has an effect on slide speed.
Hope that makes sense