In that case you more than likely don't need Java. Java Script is what is used in webpages and is rendered by the browser or in fact your PDF software that you mention. But you have to be very careful with what you allow to render with java script as it can contain a malicious payload.
Java is largely used for programs and stuff that is rendered on the Internet that runs with Java like online games and such. Java can also be an attack vector, even flash, and flash is going the way of the dodo bird in replace of HTML5 which gets automatically rendered in the browser like java script. In this day and age you most liekly don't need Java or Flash.
Since java script can be malicious, many people have use the add-on for Fire fox and its derivative browsers called NoScript. But it's very cumbersome and I don't recommend it. I used to use it but it broke many websites since a lot of websites now are JS heavy and having to whitelist things was a PITA. So now what I use for my browser is Sandboxie which keeps everything in a virtual environment and nothing touches my computer. It will also help block so-called ransomware or polymorphic malware, i.e malware that doesn't have an anti-virus definition that an anti-virus software would catch. If interested in Sandboxie then look at their website and read their forum. It's free for the browser only, but after about 30 days when you launch the unpaid version it will have a pop up screen telling you that you should buy it. Small price to pay for free and great security IMO.
There are many other proactive things one can also do to keep malware at bay. Like Faronics anti-executable. Or Shadow Defender.
Anyway... I said more than is necessary. LOL Back to the point, you more than likely don't need Java, and it would be best to just uninstall it. I would use Revouninstaller to do that so all traces are gone.
This happens all by itself, then it disappears after a couple of minutes...any ideas?