When you use a patch group it can disable the supersedence detection for patches so that's why it may be showing the older (superseded) patches missing as well. Are you also using any custom criticality filter settings in your template, and what patch type filters are you using? Does the template include software distribution? These are all things that could have an effect on the scan results you're receiving.
I've just made a copy of the default WUSCAN and selected my patch group. Is there no way to get superseeded patches removed?
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You could just go into your patch group and remove the older patches from the patch group - that way it will only scan for the latest Java patch that is contained in your patch group.
You could also look into using the Product filters rather than a patch group if you don't necessarily need to specify exact patches that you want to scan for.
Yeah i may have to remove the older patches but its not just Java,theres a lot of Adobe in there as well!
Is there not a way that you can deploy patches based on the date they were released? That would be really useful so that I can ensure that I deploy patches that are the same throughout my environments??
There's no built in way to scan/deploy patches based on the date. The only way I think you could accomplish something like this is to run your scan first, then in the scan results sort by one of the columns; either "Patch Release Date" or "Bulletin Release Date". You would then have to CTRL+click or SHIFT+click to choose the patches you wish to deploy, then right click and choose to deploy selected patches.
Also, in case you don't have the columns I mentioned you may need to add them in. In Protect you add add hidden columns to different views by doing a right click on one of the current column titles, then choose "column chooser".
I hope that helps.