Google apps engine sometimes remind me of the Java 2 Micro Edition. Even if you implement it properly there are glitches which can make your day go worse. Running on your system and running on the real server are two different things.
Seems that I have solved my "mixed-up-session" problem at the cost of platform independence. Now, my service uses google memcache in order to store my session object manually. Afterwards, I synchronize my data inside the database. Cleanups and periodical tasks will be written using google task queues.
This is a critical limitation I did not anticipate. I thought the app will be able to run everywhere. It is a small program though and still fun using the apps engine. At least I can concentrate on functional implementation and have no hassle anymore with session management.