Got any pics? Unless the roof material isn't compromised I'm not sure I'd worry too much about it...but that depends on how big or what you mean by a 'bubble'. Will condensation be an issue under the roofing material?
With Trailers, you get what you pay for, unfortunately...and sometimes the dealer charges way more than the trailer's worth. I don't think Jayco's QC issues are much different than any other trailer within the same price range..competition is pretty fierce in the RV business (imo). I've been generally pleased with the warranty, even given the silly issues we've dealt with on ours; not so happy with the dealer, however...
3 kids and Buddy the Dog;)
2010 JayFeather 23K
05 GMC Envoy XL