Vlad,
I've found the root cause of the problem and thought I'd let you know.
Since I first reported this other applications gradually started to have problems. The common factor was that like AVS Converter they could max out one or more cores on the CPU.
I spent some time analysing this and found that at some point after a few minutes of a core running at 100% and with maximum SpeedStep, something happened to ACPI.SYS. Suddenly it would cause DPC's to take up to 5 milli-seconds instead of a few micro-seconds. The knock-on effect of this on the network, storage stacks and the video driver was to bring those to a crawl.
It seems that the fans were struggling to cool the CPU and the GPU and this triggered an event in ACPI.SYS where it probably tried to slow things down in order to bring the temperature back down.
I've changed the position of the machine in order to allow a much better airflow and it looks as if it's working as expected again. It's probably that AVS Converter being able to max out all 8 cores was the first application capable of causing the system stress. Less intensive apps began to trigger it as gunge built up in the fans and reduced their effectiveness.
Best regards.