Roofing material for flat slope western pacific northwest
Your shingle manufacturer (CertainTeed) specifically states that your roofing material should not be used for 2:12 pitch (which, BTW, is not flat as you state in your question). However, the instructions also seem to contradict that later.


  Limitations: Use on roofs with slopes greater than 2" per foot. Low-slope applications (2" to 4" per foot)
  require additional underlayment. In areas where icing along eaves can cause the back-up of water, apply
  CertainTeed WinterGuard™ Waterproofing Shingle Underlayment, or its equivalent, according to
  application instructions provided with the product and on the shingle package. 


Bold emphasis mine.

Now, it is listed for slopes greater than 2:12 but with specific instructions for underlayment on "low-slope" applications.

I would pay a contractor (not the one that did the warranty repair) to ascertain the exact slope and for them to put it in writing; tell the contractor why.

If it is:


not greater than 2:12 you should demand a complete reroof by sending the home manufacturer a certified letter accompanied by the contractor's statement. If the builder does not respond have a lawyer send them a letter. If they still do not respond take legal action.
greater than 2:12, have the contractor ascertain whether or not the proper underlayment methods were used. If not, see above.


There is also the question/problem of ridge vent removal. The manufacturer specifies the use of ridge vent combined with soffit venting; however, if the vent configuration meets normal standards for your area and roof size maybe that's not a deal-breaker.