Yes, I've had a case of 'no user6 content' as well.
On my local machine (where I am developing a site - not yet public), using the eg_xxxx templates, I can't seem to place anything in user6.
I do remember in the past, when playing around, I removed or unpublished smooth gallery from this location to just see what a 'plainer' looking site would look like but I cannot now seem to re-establish this component to be displayed. Again, I too thought it must be something specific with smoothgallery but as an experiment I have just changed "Urgent News" from "Right" module (where it could be seen) to "User6" (where it does not appear). Changing it back to "Right" module and I can see it again.
AFAIK, I've done everything I should be doing, but I too am a bit stumped about this - thought it was just me and something erroneous I must have done (perhaps I have?). For the time being I was ignoring the problem (like an ostrich;)) and was probably going to re-install the edugeek package again.
If there is any advice/help out there on this problem, I would be interested to hear.