Today I reindexed all Indexes with more than one primary shard. Now every Index (including the system indexes) has one primary shard.
After that the system was stable.
Of course, when we go productive with a multi-node-cluster, I'll change it back to two primary shards.
A strange fact is, that when I use the Reporting Tool, a new Index with five primary shards is created. Then elasticsearch freezes again. But when I create a second report, which is stored in the same index, then it does not freeze.
I don't know wether it has something to do with the shard-count, or maybe with something like garbage collection.