Windows 7 32 bit, up to date, Intel i7 860. (For some reason the company runs 32bit Windows everywhere.) I tried to update all motherboard drivers etc. as far as possible.

I have a performance issue with a machine which appears in connection with multithreading (or so I think).

As an example (and where I most often see it, but it appears on other programs as well): ProteoWizard is a file conversion tool for mass spectrometry files. I can add a list of files and it will attempt to process up to 8 files in parallel (quadcore x 2 threads/core). If I choose 1 to 6 files, I start the process and it goes straight through. If I have >=7 files in the queue, conversion goes to ~20%, then gets stuck for 15 seconds, then continues again, always in "chunks" of a few % before getting stuck again.

During the time the process is stuck, CPU is at 1%. RAM is not limiting, it is maybe at 70% or so and not going up.

I don't get the same problem on other, even slower machines.

The computer gets also stuck at 1% CPU doing nothing on other occasions, but for multithreading it is most frequent.

Where should I look for the problem?