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Substrate rotten?

I set up my tank about two months ago (30 gal.) with a flourite/sand
substrate.  I've had great results -- explosive growth and amazing red
colors (although the pinker shades are a little washed out now, since I
added a Coralife 10,000 K bulb!).

However, I suspect that my substrate is rotten -- every time I disturb the
gravel, it sends up bubbles, and a few of my stem plants are browned at the
roots.  I've always had the bubbles, but I didn't notice the roots until
last night -- and the bubbles seem to have gotten worse.

I stirred up as much of the substrate as I could last night, to check the
various plants' roots and to see where the pockets of gas came up, and it
seems odd that the plants are to be doing very well over the worst pockets
of gas (under a crypt and some walleki (sp?)), and the areas of the tank
with browned stems don't appear to have much gas (under macronda and hygro).

I have another problem with the hygro, which I didn't suspect was caused by
the substrate until last night, either -- it's sending off roots from the
middle and upper sections of the stem.

Does anyone have suggestions, short of breaking down the tank?  And if I do
break down the tank, how do I prevent this?  It's my first tank setup with
sand, could I have the proportions screwed up (the proportion of flourite to
sand is about 70-30, maybe 60-40)?

I've been treating the tank (gourami had parasites, and I decided to treat
the whole tank because a few other fish had spots and fin damage) with
Maracyn, MarOxy, and a copper medication (I can't remember the name,
something like Marine Safe). Could this be aggravating the problem by
wreaking havoc with the bacteria in the substrate?