Hi Ro,
I'm not aware of any changes in v201409 that would cause this. Are you excluding
zero impressions? If you have a large # of keywords with zero impressions then the report could take significantly longer, although that behavior is not version-specific.
On a similar note, did the structure of your campaigns change around the same time of the upgrade? For example, did you remove a large # of keywords?
Also, have you tried running the same reports that are timing out in v201409 against the v201406 endpoint?
Thanks,
Josh, AdWords API Team