Google Bug or is this normal?

So at the begging of September I was hit by some sort of penalization/sandbox I don't yet fully understand (if is there someone with strong SEO knowledge - I'll apreciate if you could explain me).

My site was tracked with gA and was present on GWT. GWT was linked with gA also.

Now the thing is after that incident they kinda display different statistics:

http://i.imgur.com/LQcpaMy.png
this is the gA screen under "search engine optimization > queries"

and this is the screen from GWT
http://i.imgur.com/SozrHQb.png

needless to say that after the penalization/sandboxing I lost all my important keyword serps and currently rank only for some long keywords - so the second screen from GWT it's more accurate - yet i'm intrigued by the data shown in gA - where is that from? is that some sort of bug? is this related to my situation of beeing penalized/sandboxed?

also other thing that I've noticed and don't know how to interpret is this graph - http://i.imgur.com/LWOA0mh.png what the heck does that split means? because starting from that day the serps went down.