I have the same problem with my '08 SEL and it is unrelated to the remote start as my 5-speed manual does not have it. It isn't consistent, but does seem to be more prevalant the colder it gets ... for example, didn't happen last night or the night before; we're in GTA.
OTOH, my wife's '09 (Dec. 2008 delivery) does have the factory remote start, but we haven't yet experienced the problem of the EATC shutting down overnight, regardless of the temp ... so perhaps they fixed it for '09.