Why would they need to be converted, they are decoded to raw audio and burned to disc, that's what the codec does (converting to another format would require using two codecs).
I'm wondering if there's too much gain in the files, or maybe AC3Filter is adding gain? I don't know why AC3Filter would be used for flac, perhaps if you open AC3Filter config and under system change the filter merit.
You may be on to something; it does sound like the gain is way to high. At any rate, I'm not sure what the software is or isn't doing, or what changed from a month ago, when I was getting great CDs from ImgBurn. BTW; I've been using Express Burn, and the CDs have sounded fine with that software. Maybe ImgBurn got fouled up somewhere?