Ok, finally I figured it out. No where on the site are there any clear instructions as to how to correctly use dt. How was I supposed to know that to make a perfect timer all I needed to do was have "Every tick -> add dt to system clock". That's it. Fixes everything. It's so simple, yet I had to piece this info together and narrow down my problem to the system clock event. Before I was telling it "Every 0.1 seconds add 0.1 to system clock".
It seems to me that my original method should have worked because I thought that the internal timescale of Construct 2 already was independent of the framerate. Obviously it is not, and I couldn't find this info under the dt section in the manual. Construct 2's own time counter is not framerate independent, kind of making the whole time counting thing useless.
Also, I'm a little disappointed that in a week, no one was able to even make a reply to this thread. In the past, replies have been fairly swift and helpful. Is everyone on vacation this week? I was out of town without consistent internet and still visited this site a few times from Kinko's and borrowing my neighbor's internet by standing across the street.
However, I forgive you all. Maybe you saw "music" and "sync" in the same title and avoided it, knowing that audio support still isn't that good. For now, I seem to have fixed the problem on my own, but I'm still a little disappointed at the lack of response.
Please feel free to check out the game. I'll go ahead and showcase this in "My Creations".