Your GoJoe profile contains your all-time GoJoe statistics including all activities that you add to the app.
If activities are showing on your GoJoe profile but are not counting within the challenge, it may be that your challenge creator has set the challenge to include some but not all of the supported activity types.
Alternatively, the activity may have pre-dated or post-dated the challenge start date and time - or the challenge ended before you added or synced the activity (once the challenge ends, the standings freeze and no more activity will be capable of being added which will count in that event).
Please check that the activity is included in the challenge and falls within the challenge period.