I post it here, 'case maybe it'll help to others: yesterday I upgraded from 21.00 to 21.80 (to be precise I set the watch to auto-upgrade and started syncing in GCM, then I went sleep, and forgot about it) Today I went to my usual multi-sport activity and when I tried to change between the sports I didn't find Tabata, and started to look for it. I realized that I see all the existing built-in activity types on the watch, and I don't see any of the activities I downloaded from CIQ store.
After the workout I remembered that maybe this has to do somethign with the upgrde to 21.80, and indeed checking in the system menu I see 21.80. I have to add that I did not see any popup telling me to restart the watch, so I did not restart it. I did not get any notification as I remember from before that a new version is available... So the update was done not only automatically but also kind of transparently.
But then, just to be sure, I did restart the watch a few minutes ago, and walla, all the activities are back to what they were previously, I see them in the order I set them and only the ones I set, not all the unrelevant built-in activities, and I do see the ones I downloaded from CIQ.
UPDATE: the exact same thing happened today (that's how I discovered during the workout that yesterday night it upgraded to 22.10)