This is a chrome feature, I saw it on andoid 4.4 4 first, in the chrome beta..
I circumvented this by an xposed module:
So I kept having this after re-flashing an AOSPA rom, and solved the problem through xposed. I used the XHaloFloatingWindow module, and in "Popup Behavior" there is whitelist/blacklist option at the bottom, I just set it to blacklist all apps, only allow white listed. I don't use the whole floating window, so have no whitelisted apps. Chrome works perfectly now.
In other news, any news on when AICP will go stable on LP? Like a stable build
but use latest nightly