As I said earlier , you can get stuck in a bad part of the google infrastructure. They could have some heavy processing running, or
some sort of failure in a few boxes, and it doesn't show up on the system status, and your other instances aren't affected
as they live in a different part of appengine infrastructure.
Add some debug logging at the very start of your app (before imports of custom code) etc.... through to startup.
You will see you are probably not getting past some initial imports in a timely fashion, and it has nothing to do with your code.
I had this sort of problem years ago ;-) In the end I had to move the instance to get out of the performance hole. I was getting hit
with DEE on startup and if I could startup it was slow or DEE'd at the same time every day for about 3 hours. On other occasions it the DEE where continuous until someone at google noticed they where having a problem.
Rgds
Tim