Why is a metabisulfite / starch / HCl solution unstable?
I can partially answer the question. I know what is happening to solution B. I don't know of a more stable version.

One potential problem is the acid-catalyzed hydrolysis of the starch into glucose, which does 
not form the blue complex. 
$$\ce{nH2O + (C6H10O5)}_n \ce{-&gt;nC6H12O6}$$

For the timing to be off, the metabisulfite must also be decomposing, either by reducing glucose or by reacting with dissolved oxygen. I'm not sure what the specific process is, nor do I know how to stop it.