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Thanks to my mate Hannes for his cvsSynchCheckout script (archived here) which solves many of the problems created by the "intelligence" in cvs commit and cvs import.  Here are two problems it has solved for me thus far:

1. cvs import will not add any directories called "core" to the repository.  I'm guessing this is because it doesn't want to checkin a core dump, which is all well and good, but why the fuck it doesn't check whether core is a directory (and hence clearly not a core dump) is beyond me.
2. Our code in work switched from using Linux kernel 2.6.25 to kernel 2.6.27, hence we wanted HEAD to reflect the 2.6.27 kernel.  Trouble is that some files are moved in 2.6.27 so we needed some files deleted and others created.  cvsSynchCheckout to the rescue!

Here are the instructions according to Hannes...

Note:  The script doesn't do anything as such except print out the list of commands needed.  So dump the output to a file, verify it all looks good, then execute the file with sh.  Once the file has executed you will need to call cvs commit to make the changes permanent.