i never use programs for that sort of thing pm your keywords and site il take a look if you like Looking at offering some free seo advice to build my portfolio
Most likely you just don't have enough quality backlinks to your site. I agree that there isn't any decent software that can effectively diagnose ranking problems.
Using program to analyze the website is helpful as it analyzes the site for Validation, broken links and images, download speed etc.. You must correct the things pointed by the program. After doing it, you must analyze the site manually if the site is not too big.. Coming to your problem: I think you should use Google Webmaster tools. It will show the position of your site for the kewords searched in past week or month and so.. Doing a Manual check for the position in search results is good as you will get some idea by looking at the titles of the high positioned results. I suggest the method I follow to check the position manually: 1: Set the preferences in Google to display 100 results in a page. 2: Do a search. 3: Use the Find feature of the browser to check for your site in the search results. 4: If found, count the position manually. 5: If not found, go to the next page of the search results. 6: Check for your link in upto 4 search result pages (400th position) if not found in initial 2 pages. If you wish you can check many more result pages. If you dont find your site listed even in 4th page, it means your site is relatively not optimized for the keywords. And now you must use a program to check your site's position as it takes a lot of time check through more result pages. One of my site is in 110th position for a single keyword, but in 20th position for 2 keywords and 5th position for 3 keywords. I found this in Google Webmaster Tools. I checked it manually also..
there is no tool that will do a complete analysis of your site and give you a detailed report. you need professional SEO analysis service for that. however, you can try the link below which might be of some help http://diagnostics.googlerankings.com/website-diagnostics-panel.php
Any "company review" will use software to obtain their results. But it is the experience of the company's staff that makes the difference. It's the review of On-Page Optimization, Off-Page Linking, Site Design, Keyword Selection, etc. And finally, putting this information together into a "plan" that makes it important to use a company.