Sounds like a now smaller invisible frame over your PopButtons.
Sorry I do not have any other ideas about that than Aviana.
There is an addon called Where is my cow here on wowace with which you can show what frame your mouse is over.
You might consider temporarily installing it to find out if our guess was right.
I had this once with Autobar, which I would call a usual suspect on these things because it creates 32 buttons per default even for class bars which use 4 or 5 only. If you do not change the number of buttons there is quite a huge invisible frame hanging around. But this is just an example, I do not intend to call Autobar Mr. Evil I use and like it myself :)
I have gotten to skin the Buttons but eliminated the cooldown and got those annoying marked on active borders with that I think ;P
Was hell of a lot more reqs to support Bf than I had thought.
I had tried to port Numen to Ace3, but getting rid of AceOO just got over my skills I got to admit.
Sorata has basically done that (working^^), plus making it general.
Options etc. were all finished (basically no prob to use AceConfig3 and AceDB3 in Ace2 Addons because they are Libstubbed).
In the long term I would vote for improving the Totem Module inside Poppins to get the features of Numen (well, the ones that actually have to do with the buttons themselves). "Automatic" Totem Setup and destroying totems on right click should be doable inside such a module.
The reason I would vote for this is basically: Less work. There is a main dev which is well, at least a lot better than myself and one had to look only for totem related stuff inside a module.
The other options would be a) ignoring the other addon and continue dev or b) manually porting the nice stuff of Poppins like the Ace3 stuff and AceOO-less prototyping over to Numen which would induce possible work anytime Poppins gets updated.
Noted: For the long term and my point of view.
Short-term related Numen actually works fine, just to mention that :) Besides, anyone is free to do what he wants it is just me saying I will not try to get things like Bf support to Numen because I would too much feel reinventing the well like now.
For BF compatibility and the request about Buttons not popping up, you might want to check out the thread about Poppins by Sorata which is basically a general purpose Popbutton addon with some Numen code in it (like the Totem timers).
I dunno about the anchoring but I have an option on my weird local hybrid twin to turn tooltips (off/on/combat).
If that is ok for a while I would at that to the live version.
About the showing popup totems thingie I am aware of that wish.
I personally would like to make it customizeable how many totems per row are shown but that will be quite tricky for me since I cannot help not really getting into the lua oo approach or maybe it is because of working with someone elses code.
Showing all of them should not be much of a problem though, if that is what you would like I could add an interims option if I get that to work without much of a hassle.