There isn't a perfect way to create your meta tags therefore the analzysis results will vary from tool to tool - some will like your code and some will not - as long as you don't see warnings in every one of them - don't worry.
The backlinks thing is a completely different story. The results for any particular SE should not be different no matter what tool you use, because every backlink checker does exactly the same thing - it asks the SE for:
link:www.yoursite.com.
The number of links shown in Yahoo and MSN will vary from day to day and sometimes from hour to hour. On the other hand the number of links shown in Google will remain the same for the whole month and then it will be updated. But even after the update Google will not show all your backlinks but just some (bigger rather than smaller) part of them! Confusing? Well, it may be
You must also know that Yahoo will count your backlinks in completely different way than Google - e.g. if you make a site-wide link exchange with 100pages website, then Google will increase your backlinks number by 1 or 2 while Yahoo probably by 100. Therefore the numbers at Yahoo are so much bigger that those at Google.
This is the backlink tool I like:
http://www.mikes-marketing-tools.com/link-popularity/