According to Troy Renk on 104.3 the Fan it was a basic disagreement with Elway who wanted to integrate IPO stuff like other teams like the Chiefs have, with the offensive concept, and Kubiak who resisted and wanted to run his old offense.
They couldn't agree, because Kubiak and Elway were talking and "Elway wasn't getting the answers he expected to hear" about changes he wanted made to the offense.
"We now are going to get a new offense in Denver." -- Alfred Williams.