Beth, this is a complete shot in the dark, but if it is a systemic fungal or bacterial issue, there are two approaches you might consider:
One is a copper treatment of some sort - Phyton 27 is the most common product used, as it is - to a degree - a systemic fungicide/bactericide. I have no first-hand experience with it, as I avoid it due to the fact that some plants (some dendrobiums and most thin-leaved types) don't go for it, and to some, it's out and out toxic.
The other is a biological control. The colonies of bacteria and yeasts in products like Inocucor Garden Solution can actually colonize the plant as well as the medium, protecting it from pathogens and actually eliciting some self-protective responses.
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