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If a conference does poorly in the CFP does it impact future close decisions?  Should it?

Is the SEC champ a virtual lock as a result of this?  Imagine one is 11-2 with an OOC loss versus a 12-1 alternative?

Does this hurt the B12 and Pac teams in a close decision?

First, I want to second everything that @Kris60 said.  I agree entirely except that I am a little more open to it being a valid criteria than he is.  

Is the SEC champ a virtual lock as a result of this?  

I think this comment is too narrowly focused on the SEC Champion.  No, I don't think that the SEC Champion is a virtual lock.  There is, of course, a possibility that a relatively weak SEC-E Champion with multiple losses could upset a relatively strong SEC-W Champion in the SECCG.  In that case I do NOT think that the SEC Champion would be a "virtual lock".  

Instead, I think the issue is that there is a near certainty that at least one SEC team will get in regardless of whether that team is the SEC Champion or not.  

Does this hurt the B12 and Pac teams in a close decision?

I think it does, but only in a close call effectively as a tie-breaker.  I do NOT think that a 1-loss non-Champion Ohio State would get in ahead of an undefeated or one-loss B12 or P12 Champion but I absolutely think that a 1-loss B1G Champion Ohio State would get in ahead of a 1-loss B12 or P12 Champion.  

If Conference A gets whacked in the playoff five years in a row, should that be a factor in year six?

It shouldn't buut it will, and it won't necessarily be deliberate.

If Conference A gets whacked in the playoff five years in a row, should that be a factor in year six?

the answer to the original question is, "Yes"

the answer to this question is, NO it shouldn't be, but it will be a factor in year 6

I don't think either are big factors, but when everything else is equal and the committee is looking for a tiebreaker, it is a slight factor.
A "slighter" factor than politics and TV ratings

If Conference A gets whacked in the playoff five years in a row, should that be a factor in year six?

No.
.
The only thing that should happen, and it would take a lot more than simply their champion losing every year in the playoff, is if a conference is deemed too weak to even be included as a P5 conference.  
Otherwise, absolutely not.  
.
Look at Nebraska from 87-93.  If someone magically said the Big 8 champ gets left out if it's Nebraska again, their 3 NCs in 94, 95, and 97 don't happen.  But as I said, if it was deemed that the Big 8 at that time was too weak, and a new deal was being put into place, then you'd exclude that whole conference, not just the one team.  The Big 8 was never that weak.  You could make the argument that the Southwest Conference was, during its last 5-6 years.  It had NOTHING but A&M at that time.