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The buff/debuff problem will involve a rewrite to make it work with blizzards changes to make them secure frames. nUI6 should resolve this issue ( hopefully ). The only work around is to install Scotts aura button plugin for nUI to replace the bars on the lower left and right with buttons. These then let you have tooltips. The ones in the hud area though is a bit more complex. These involve editing the layout file for the specific hud display you use and adjust the enabled flag for the aura sections. There are various threads regarding how to do this elsewhere in these forums. The reason why by default they don't display tooltips is to not mess up the people that click their targets and thus need their hud to be click through.
The loot drop problem has been around for a long while. Not sure if it has fixed itself as I didn't have the problem when I ran a couple of Pandaria dungeons yesterday. I might have been just lucky though. But from what I can figure is that it is a layer problem. I'm not sure how easy it is to change that aspect though without messing other things up at the same time.
The special action bars have all been resolved in the nUI addon with the extra action bar currently fixed using the files I have adjusted and posted in the thread in my signature. These changes will ultimately be put into nUI5 the next time Scott does an update but while he is working on nUI6 I will be keeping an eye on keeping nUI5 working in the mean time.
As to auctionator. Can you post up the error message that you get the next time it triggers. I don't use it myself at the moment but I vageuly recall seeing it as a useful auction tool and I believe my warlock will probably need it at some point with her tailoring and inscription sales and my druid with her herb and alchemy sales. Only time will tell. But hopefully in the mean time I will be able to spot what might be causing the problem.
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