Don't use those software (Rank tracker) use an automated rank tracker like SERPBook can gives you a instant overview of all of your keywords' rankings in a glance, from there you can use SEO and boost the keywords that are having low rank position on Google.
You can find rank tracker here, new version and it works without a lot of hassle!
Code:
http://bestblackhatforum.com/Thread-GET-Rank-Tracker-Professional-7-11-4-Multilingual-Key
You can also track keyword rank with Scrapebox + the Rank Tracker premium plugin for it. Ideally, you would also need some private proxies to speed things up, but even without any proxies, I've been able to pull a rank report on up to about 100 keywords or so each day, by simply setting the delay to about 60 seconds.