After a couple of hours of hair-tearing...
The basic advice to remove the ws=win32 flags from the feature.xml and plugin.xml files (for mcsdk and pdk) as per [url=http://e2e.ti.com/support/dsp/c6000_multi-core_dsps/f/639/p/297968/1040381.aspx#1040381]this post[/url] is correct.
However Eclipse seems to maintain a private cache of information from these files (I haven't found it yet!) and thus if they are corrected after a failed installation attempt Eclipse does not pick up the changes.
There is a workaround, which is to create a subdirectory of in your TI installation directory, and move the now-modified mcsdk_2_01_02_06 pdk_C6678_1_1_2_6 directories into it. Then tell CCS to scan this directory for new products.
In CCS6 which I'm using, this can be done in the Preferences window (Window->Preferences), under Code Composer Studio->RTSC->Products: add your new directory to the Product Discovery Path.
I believe that it should be possible to remove the dud repositories from Eclipse - which most likely eliminates the need to create a subdirectory - but haven't yet found a way to do so.