1) No, I would not use [b]Alg [/b] - I am actually surprised it does not issue an error message. Rather [b]RK4[/b], which will be extremely slow but may be good for the initialization (and only for a limited time horizon); then [b]VODE[/b].
2) This does not make any sense - unless it's a consequence of choosing Alg as integrator.
3) What do you mean by "all particulate COD"? Only the particulate fractions that contribute to COD? or all the particulate fractions, as opposed to the soluble ones?
And do you mean: at the beginning of the simulation - which may be, again, due to the integrator? or somewhere at an early stage in your layout?
4) Nothing wrong in sharing issues and thoughts: may be useful for others too
[i]Anyway, I will take a look at your project and get back to you[/i]