@Gerenb:
You are incorrect that SQ Remote doesn't support multitasking. That feature works extremely well, as a matter of fact. When the app is turned on, it polls Vera and updates the status of all devices.
@RobertN:
If I were to make a guess, are you using WiFi when this issue occurs? Is Bluetooth enabled on your iPhone? Try turning off Bluetooth, and see if that clears it up.
This is apparently a bug in iOS4, and Square Connect has been working hard to design around this bug.
Hope this helps.
-Robert