Hi Mark,
We were experiencing similar behaviour and contacted Apptio about it. They have pointed this towards a potentially 'known' Microsoft problem as the cause, in the 'costs for export' area.
I have contacted MS regarding this (early June) for our subscriptions and have only recently had an MS ticket assigned. I did notice a subtle improvement recently in Cloudy however.
Previously, choosing 'last 7 days' only presented 5 days of data, we are now seeing 6, so a slim improvement, but definitely lagging by 36+ hours also.