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I have a site with advagg-6.x-1.x-dev and ubercart-6.x-2.9 (had same problem with ubercart 2.7).
If I enable jquery_update-6.x-2.0-alpha1, the checkout page on ubercart breaks. The credit card payment pane gets replaced with
This only breaks in Chrome and IE. Firefox works.
?advagg-debug=1, but didn't get anything in the watchdog log.
When I disable advagg, both jquery_update and ubercart work.