SalesforceLabs
Receive alert if the app is left running and idle
Receive Alert > [Cancel][Retry] popup when moving between objects. If I log out and then log back in I no longer see these alerts.
If I leave the app running with no activity overnight and then go to view records it starts occurring consistently. We are going to train to this issue by logging out.
This sounds like the salesforce session expired and the app is having trouble refreshing it. This is tricky in SFiPad because the app uses both the SOAP and REST APIs, either one of which could expire at any time, and when one is refreshed the other one needs to be updated too. I definitely need better handling here.
There's also another issue here, where records owned by the internal "License Manager" user show up just fine in the web UI but cannot be queried over SOAP or REST and will result in errors very similar to the ones you note here.
I've included this as an unsolved problem in Salesforce for iPad's readme (released today along with the source). See the main project page.