if you press the "show collections" button twice it shows everything again? if you uncheck "enable collections" in properties->general and restart the program does it happen as well?
what are other settings threads (the blue plus sign toolbar button) are enabled or not?
maybe you have "new" checked in the quick filter bar?
how long it takes until the view starting showing only few items?
also if a newsgroup is unloaded (it may happen when it finished download headers and it is not open separatedly, although the behaviour can be changed in settings) the associated entries will disappear from global view.
if not that try to email me some screenshots
