Hacking Mother 3 Help?

[DoubleD45]

Sorry if this isn't the right place to post, I haven't been to this website in 3-5 years.
Ok, I recently purchased a Supercard DSTWO, and I haven't had any major problems with it besides running this one game perfectly.

First of all, my primary Micro SD is a Kingston Class 4 8 GB SDHC card (bought from Amazon) and I've been using the reader included with the Supercard DSTWO
I am on the latest EOS (Supercard DSTWO EOS 1.11 12-24-2012) and Patch (12-06-12)
The emulator is version 1.21 and game_config.txt (the exact name, no numbers, etc) is in the NDSGBA folder.
I've tried both the non-translated, clean rom, and translated version of the game on 2 different micro sd cards, and they've both yielded the same results.
I've reformatted my Micro SDHC with SDFormatter v 3.1 and did a fresh install of everything after I first tried to run the game and had problems with it and still have the issues.

This is my third time playing through the game but first time playing the fan translation on actual hardware and I've played up to the first save point. The title screen, naming screen and intro had audio popping, but the game seems to run flawlessly besides audio issues. One of the things I love about this game is the music and I'm worried that this will be an issue throughout the game (The music outside Alec's House, Mom's Hometown, has very minor audio issues, so that's a good sign I suppose).

So, here are my questions:
1. Is the terrible audio popping on the title screen normal for the Supercard DSTWO?
2. Is it normal for the audio to randomly switch from ear to ear on the naming screen and intro music? I played the original japanese cart on my DS Lite last year and I know the songs don't normally sound like this on actual hardware using headphones.

 

[goemon_guy]

Adjusting the frameskip to automatic seems to eliminate some/most of the audio irregularities for me.

Other than that, the GBA emulator on the DSTWO isn't exactly all that accurate when it comes to that stuff.
It gets the job done, though.

As for your second question, I'm not exactly sure what you mean. I've never noticed anything like that.

 

[DoubleD45]

The Frameskip is on Automatic by default, I guess I shouldn't have used the word terrible, because the Manual setting makes it 10x worse.
And I believe my second question is badly worded too, it doesn't seem like the audio is so much as cutting out as it gets louder in one in ear and quieter in the other, for about a second before it switches. I've only played one other game on the emulator and it didn't have this problem.