Ferric Chloride is VERY easy to contaminate. If you sprayed anything such as WD40 around it when the lid was off, even a tiny droplet can cause problems. A single droplet of windex in a container of Ferric with kill the entire container. Ferric will "break down" over time, but it takes a LONG time. Often as much as 2-3 years. Most folks tend to end up with it contaminated before it breaks down beyond use.
What you describe sounds more like a "clean" issue.... Anything you intend to etch in Ferric must be absolutely clean. Personally, I put on latex or nitrile gloves..... clean the item I'm etching with acetone, then again with windex..... and FULLY dry it. I also use a clean paper towel to "wipe" off the surface of the ferric.....if you see ANYTHING, even a discoloration floating on the surface of the ferric, when you place something into the ferric, the surface tension will cause whatever it is to get onto whatever you're trying to etch.... that is the most common issue that folks have.
Something that causes many folks problems, is the type of rags or paper towels they use to clean items for etching. If you use typical household white paper towels, they will leave a slight "rainbow" colored haze sometimes..... this has to do with the chemical used to "bleach" the paper for the towels. I generally tell folks to use ONLY the Scott Shop Towel brand of paper towels (the blue colored ones).... they do not leave any residue. If you use "rags", they need to be 100% cotton.... especially if you use acetone to clean.....acetone will "melt" most synthetics, and leave a film on anything you're trying to etch.
In the end if there is an uneven etch, or spots as you described, it's almost always a clean issue. OH! One more thing is the temp of the ferric. Ferric works best for what we do in the 70-80F range..... higher temps generally aren't a problem, but if the ferric is cold (below 70F) etching slows down dramatically.... I doubt any of that bears on your situation, but it's worth mentioning.
Keep us posted!