Enlightenments systray module has always been buggy, sadly. I have noted similar issues myself. There is a newer version of enlightenment now tho but I wouldn't expect these issues to be fixed. From what I gather e development has been on a new module Bryce which among other things is expected to have the potential to replace the systray so I doubt i could even interest any e-devs into looking into this issue
The systray is obsolete in their minds and that is paraphrasing a lot a talk I had with Raster on systray issues. I could perhaps look into it myself but I don't know alot about how the systray works and underlying libraries it uses. Plus it seems I can't even catch up on other tasks I am trying to accomplish.
So I am not really sure what to tell you sixtharmy other than I would expect there to be less problems on a non hidden shelf. But still I have noted issues even then. And of course no problems if you don't use apps that rely on the systray. Neither of those are really great advice.
For the record tho at some point I am going to try to update both elf and enlightenment in the testing repo. I am waiting for efl and python-efl to be 'stable' enough. And by try to I mean if updating efl doesn't do serious breakage to our current set of efl apps. If it does break our current set of efl apps then updating efl will have to be delayed until we (mostly me) deals with the issues caused.