Thanks for your reply, no I don't think that the old pages had better on the page SEO.

I'd love to post the URL, but I'd rather not have my client and colleges reading my forum posts by following referring URLs

I'm certain the issue is that my two main product index pages on the live site are in the sup index, I'm sure once this issue is sorted the rankings will follow. Originally the content of these two product index pages was just a copy of the two home pages from the old domains, 301 redirects were put in place to direct visitors (and search engines) from the old home pages to the new product index pages.

After a few weeks the copy on these pages was rewritten as I suspected the reason they were in the sup index was due to the duplicate content (even though 301s were put in place). Since then the copy has been spirded and cached, but they still drift in and out of the main index.

However, today I have just performed a site only search in Google and both now appear to be in the main index at the same time, so fingers crossed it will stick and the rankings will come.

The redundant 2 domains do not rank for any searches now (haven't for about 4-5 weeks, but when you do a site only search there are still 35 pages (from an original 160) listed, although the home pages have gone. However I'm just paranoid that until ALL the pages are dropped it (Google) will still somehow 'remember' the home pages.

The silly thing is when I read posts like this, I think "just give it some time man!", but when your the one with a boss breathing down your neck doubting your abilities if can be very frustrating to say the least.