This video really helped (comes from the first page of this thread), although it's for capturing legends/wild PKMN - it still explains a bit about finding your DS parameters:
http://www.youtube.com/watch?v=T4zNQH9cC3w
Q1: Timer0 is just one of those "parameters" - something specific to your DS (and the seed you hit)... It's usually constant for what you're trying to do. For example, when trying to RNG my Reshiram with Method 5, Standard Seed, Stationary Pokemon, my Timer0 is C7C. Very occasionally, it will fluctuate to C7D or C7F, but it's mostly C7C for me... So, I search for a seed with Timer0: C7C... If it fluctuates, I'll miss my seed - this is what may be happening to you. So you might want to try searching with other Timer0s if you keep missing your seed, especially if you're pretty sure you're doing everything else correctly.
Q2: I'm not sure there's a way to "fix it" - rather, you just have to try a couple of times, and see which Timer0 you're actually using when you hit a seed (note the IVs, for example, of the wrong seed you keep hitting, esp. if it keeps coming up)... There's a "min Timer0 / max Timer0" blank you can fill for the DS Parameters, which you could use to widen your range for Timer0, in case it's not what you've currently got in that blank. Doing so could help you find out what your most common timer0 really is.
EDIT: Oh crap, sorry - you actually can't check the IV of anything 'cause you're RNG-ing for your TID/SID. In that case, it's really just a matter of guessing and checking with the Timer0 until something shows up and matches with what you're getting... unless someone else has a better suggestion?