How do I batch update a standard custom field for event participants?
From the description of your custom fields as "normal custom fields" and your current workaround, it seems that the fields you want to update are contact custom fields rather than participant custom fields.

If that is so, then do an Advanced Search specifying criteria in the Events section rather than a Find Participants search. On the results page you will have the option to Batch Update via Profiles. Select that option and all your profiles should appear in the selection list.