I've noticed this bug a few times,
The bug happens when (for example) you open patchmypc and Java shows up in red on the right. But you realize you don't need java anymore. so you proceed to uninstall it.
After it's uninstalled click refresh in patchmypc and it disappears from the right column but stays checked on the left column. You think it's gone from the right until you click on the update button it then proceeds to update java anyway.
One more bug I noticed is the 360 total secure bug, where no matter what it always shows up in red on the right.
Sorry for the late reply,
If you closed and open Patch My PC after removing Java, is it still selecting Java or not?
About "360 Total Security", Do you use an app with a name that is close to "360 Total Security"?
I've attached a screenshot to show the 360 total security issue. Sorry for the crappy quality. I had to resize it smaller to fit under the file size requirement for attachments.
I also found another issue today. I opened Patchmypc. It said I had out of date applications, one of which was itunes. I left patchmypc open updated itunes using the apple updater and then hit rescan on patchmypc and it turned green. But when I hit perform updats it started downloading itunes.
Looks like your 360 Total Security is not the latest as the one in Patch My PC, Maybe v8 doesn't upgrade to v9. Can you remove it and install it again and see if that fixed it? and we will see if there is something we can do about it anyway, and we are look for the other issue as well.