This is still confirmed on debian wheezy. System: RAM 64 GB CPU Dual AMD Opteron(TM) Processor 6212 (16 cores in total) 2x SSD in RAID 1 256GB 2x HDD in RAID 1 1TB
With the innodb_buffer_pool_size on 50G the timeout is way too short. We've fixed it with the same proposed fix by the original bugposter.
