I understand there may not be a simple answer to this question as it may depend on individual setup etc. But my GA search terms are consistently vastly different to my Funnelback top keywords (e.g. my top keyword last month in Funnelback was searched 299 times, in Google Analytics it was only recorded as being searched once).
I thought some variation could be down to the way they're measured (e.g. Funnelback records any amendments to the search/filtering as a new unique search, whereas in GA this might go into search refinements rather than a new unique search), but surely not a difference of 1 to 299?
Does anybody know why they could be so different? My unanswered keywords also consistently show very specific misspellings to have been searched more times than I would imagine they actually have been, so I suspect Funnelback is overreporting rather than GA underreporting.