Well, that would explain at least the 'clunk' part of the problem ;-) However, it doesn't explain the 'crawling' of the axes when EMC is shut down (or just not started, for that matter. Also does it when the computer is booted into Linux), does it? Or is that also somehow related to real-time delays? One thing to notice, though: to rule out hardware errors, we've investigated when it occurs. Right after loading the kernel image (before mounting the file systems), the crawling starts. With a stock (i.e. non-real-time) kernel it doesn't occur at all. Starting to suspect the kernel, here. Perhaps I should see what it does with a 2.4 real-time kernel, just to exclude some things.
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