You'll never get exactly the same behaviour on your local system and on the real GAE infrastructure. For once simply because the infrastructure on which you're running is different: OS, hardware and network performance/capabilities, performance/capabilities of the actual vs SDK-simulated google APIs and services your app may be using, timing, etc.
A few examples (they're from the standard env GAE, it's true, but it's fundamentally the same idea):
You should investigate the differences - you're more than welcome to ask questions about each one of them right here, on SO.
In general you'll find the differences falling in 2 categories:
plain performance differences, expected, but they may uncover actual problems in your code: race conditions, wrong timing assumptions, etc
functional differences - to find general areas where you want to perform testing on GAE rather than locally.
For example I learned (the hard way) that the SDK datastore emulator doesn't emulate the contention logic from the real datastore - while locally my app was running fine, on GAE it was crawling miserably due to contention, I had to re-write a good portion of the logic to address it. See Contention problems in Google App Engine