@tedster My mistake was using a relative canonical tag and missing the /
So google used the canonical to point at non existent pages (web master tools reported loads of 404 errors)
So a page: blue/widgets/index.html
would appear in web master tools as a 404 error blue/widgets/blue/widgets/index.html
Hope that makes sense.
Anyway, its been 2 months since fixing with no recovery, should I 301 all those missing pages or just wait, and does anyone know how long I will have to wait