Sudden erroneous/inflated results from SEOBook's Rank Checker???

We have been using SEO Book's Rank Checker tool for years to monitor our organic rank for our optimized keywords, primarily for Google rank. A few years ago (when results started getting contextual) we started running the tool anonymously (i.e.: no cookies or context). For the last few years this has worked well: Rank Checker always showed our results on Google to pretty much track with what was reported by Google Webmaster Tools (at least, for the keywords that have enough traffic to show up in Webmaster tools).

A few months ago we started seeing much lower results for our top terms in Rank Checker. Keywords we used to rank 2-4 on were suddenly showing more like 8-9. Thought this was really happening for a while then started to check on our checker. Found that Google itself was giving us results of 2-4, which we confirmed:

-using multiple browsers, all with their respective "incognito" modes enables
-on multiple computers
-on multiple networks

Also, spot checking on tools like SearchEngineReports.net showed the same, much better results.

Has anyone else seen odd recent results from Rank Checker? Is my basic methodology here sound? (I know we will never seen "true average rank", but we need a baseline to judge success of SEO efforts; wealso look at actual referred traffic).

About to switch to SearchEngineReports.net if we cannot figure out what happened to Rank Checker.

Thanks - djm