I've had the same problem with my 35T, most caches showing, some not (which previously were). Sometimes they would show though, then the next day gone. WTF!
Deleted all the gpx files and reloaded them. No improvement. Files were definitely on the GPS, even added them individually, but they just did not show.
Today I checked the filters (thanks to hints from this thread), and adjusted them all to 5, and checked again. Nothing there all now! No caches anywhere?? Readjusted the filters to 1, checked again, and EVERYTHING was back, including the caches that were the cause of the initial issue.
Experimenting with filters now, lets see what else I can see.