Just a few "litmus strip" questions to start with:
- What is the exact call code that you're using to call Ola's script? (Please post it for the database in question without the name of the database so as to not expose that to the public).
- How often are you doing your "regular" index maintenance?
- Do any of the indexes that you're rebuilding have a Fill Factor of "0"?
- Are you excluding the indexes that have been rebuilt from the sp_updatestats run?
- When WAS the last time you did a FULL SCAN stats update on the indexes for the "large table" table that MS was talking about?
- What changed in the week prior to Nov 14th?
- This one is super important... you say that "every hour they are seeing sporadic timeouts". Do they coincide with any particular activity such as a scheduled job (either internal or externally controlled)?