We can't tell from Blackduck's data either since it isn't known what criteria are used by them.
We could pick other projects and see what the trend is in them, but ultimately all we would know is what the trend is in them. Google Code looks like a fairly easy place to gather some figures from and they host a lot of code these days.
Any such study is limited by the set of data it looks at. I presume the FSF chose Debian because it is (a) large (b) licenses are reasonably easily checkable (c) well documented historical versions, so they could quickly check if the there is a trend away from the GNU GPL in the kind of systems the FSF was created to create.
The changes in Blackduck's data are simply too large to reflect changes to say GNU/Linux distros, since software tends not to change license that often, so it seems likely they are just including more sources of free software from other places which simply have less GNU GPL software in them, in which case what you are seeing is their data becomes more representative of the totality of free software code rather than a trend away from the GNU GPL.
Thus it is possible both studies are correct and that GNU GPL usage is increasing in Debian (and probably other general purpose GNU/Linux desktops - not least a lot of them are based on Debian, and perhaps in general), and GNU GPL now forms a smaller part of the code base that Blackduck are keeping in their knowledge base.
Whilst I'm sure the FSF like people to use the GNU GPL, they are pro-free software, so if that the amount of free software Blackduck find is growing faster than the growth in GNU GPL software, it is unlikely to be keeping my friends in Boston up at night.
But what really matters is what software people use, not the proportion of software in repositories. I'm using Debian to write this, and I don't much care what free software license most of the software I use is, as long as Debian can inspect, package, fix and distribute it.
I care more when I write code, but mostly that the codebase I'm contributing to aims to remain free, a copyleft license is a guarantee of that, but it isn't the only such guarantee that makes me feel good. I'd happily contribute freely to the Apache project knowing me and my friends can expect to benefit from any such contribution in future even without a copyleft license.