When I run a sample query using the SE API browser (is that right term?), say against /questions for example (here), I'll always see something to the effect of:

...
  "quota_remaining": 9424,
  "quota_max": 10000,
  "has_more": true
}

Which tells me it's using a key and is not restricted by the 300 quota limit. A quick check through the Chrome debugger (or firebug) will reveal that the key it's using is key=U4DMV....

Now when I go to edit the default filter using:

And upon hitting save, I'm presented with the following:

And investigating this further in the Chrome debugger reveals:

{
  "error_id" :502,
  "error_name": "throttle_violation",
  "error_message": "too many requests from this IP, more requests availabe in 27628 seconds"
}

So basically what's happening here is that all queries generated when hitting the Run button use a key and are therefore not restricted to the 300 limit, whereas, the query used to build the filter doesn't use the said key (and is restricted). Would it be possible to update the filter builder to use the key as well?

Before someone points me to use /filters/create instead, I should mention that it doesn't appear to work for uber filters for whatever reason. Let me demonstrate:

Create a filter with the following parameters:

include:

.backoff;.error_id;.error_message;.error_name;.has_more;.items;question.accepted_answer_id;question.answer_count;question.body;question.bounty_amount;question.bounty_closes_date;question.closed_date;question.closed_reason;question.community_owned_date;question.creation_date;question.down_vote_count;question.favorite_count;question.is_answered;question.last_activity_date;question.last_edit_date;question.link;question.locked_date;question.migrated_from;question.migrated_to;question.owner;question.protected_date;question.question_id;question.score;question.tags;question.title;question.up_vote_count;question.view_count;access_token.access_token;access_token.account_id;access_token.expires_on_date;access_token.scope;badge.award_count;badge.badge_id;badge.badge_type;badge.link;badge.name;badge.rank;badge.user;badge_count.bronze;badge_count.gold;badge_count.silver;error.description;error.error_id;error.error_name;event.creation_date;event.event_id;event.event_type;filter.filter;filter.filter_type;filter.included_fields;inbox_item.answer_id;inbox_item.comment_id;inbox_item.creation_date;inbox_item.is_unread;inbox_item.item_type;inbox_item.link;inbox_item.question_id;inbox_item.site;inbox_item.title;info.answers_per_minute;info.api_revision;info.badges_per_minute;info.new_active_users;info.questions_per_minute;info.total_accepted;info.total_answers;info.total_badges;info.total_comments;info.total_questions;info.total_unanswered;info.total_users;info.total_votes;network_user.account_id;network_user.answer_count;network_user.badge_counts;network_user.creation_date;network_user.last_access_date;network_user.question_count;network_user.reputation;network_user.site_name;network_user.site_url;network_user.user_id;post.creation_date;post.last_activity_date;post.last_edit_date;post.owner;post.post_id;post.post_type;post.score;privilege.description;privilege.reputation;privilege.short_description;question_timeline.comment_id;question_timeline.creation_date;question_timeline.down_vote_count;question_timeline.owner;question_timeline.post_id;question_timeline.question_id;question_timeline.revision_guid;question_timeline.timeline_type;question_timeline.up_vote_count;question_timeline.user;reputation.on_date;reputation.post_id;reputation.post_type;reputation.reputation_change;reputation.user_id;reputation.vote_type;revision.comment;revision.creation_date;revision.is_rollback;revision.last_tags;revision.last_title;revision.post_id;revision.post_type;revision.revision_guid;revision.revision_number;revision.revision_type;revision.set_community_wiki;revision.tags;revision.title;revision.user;suggested_edit.approval_date;suggested_edit.comment;suggested_edit.creation_date;suggested_edit.post_id;suggested_edit.post_type;suggested_edit.proposing_user;suggested_edit.rejection_date;suggested_edit.suggested_edit_id;suggested_edit.tags;suggested_edit.title;tag.count;tag.has_synonyms;tag.is_moderator_only;tag.is_required;tag.name;tag.user_id;tag_score.post_count;tag_score.score;tag_score.user;tag_synonym.applied_count;tag_synonym.creation_date;tag_synonym.from_tag;tag_synonym.last_applied_date;tag_synonym.to_tag;tag_wiki.body_last_edit_date;tag_wiki.excerpt;tag_wiki.excerpt_last_edit_date;tag_wiki.tag_name;top_tag.answer_count;top_tag.answer_score;top_tag.question_count;top_tag.question_score;top_tag.tag_name;user.account_id;user.age;user.badge_counts;user.creation_date;user.display_name;user.is_employee;user.last_access_date;user.last_modified_date;user.link;user.location;user.profile_image;user.reputation;user.reputation_change_day;user.reputation_change_month;user.reputation_change_quarter;user.reputation_change_week;user.reputation_change_year;user.timed_penalty_date;user.user_id;user.user_type;user.website_url;user_timeline.badge_id;user_timeline.comment_id;user_timeline.creation_date;user_timeline.detail;user_timeline.post_id;user_timeline.post_type;user_timeline.suggested_edit_id;user_timeline.timeline_type;user_timeline.title;user_timeline.user_id

exclude:

answer.answer_id;answer.body;answer.comments;answer.community_owned_date;answer.creation_date;answer.down_vote_count;answer.is_accepted;answer.last_activity_date;answer.last_edit_date;answer.link;answer.locked_date;answer.owner;answer.question_id;answer.score;answer.title;answer.up_vote_count;.page;.page_size;.quota_max;.quota_remaining;.total;.type;comment.body;comment.comment_id;comment.creation_date;comment.edited;comment.link;comment.owner;comment.post_id;comment.post_type;comment.reply_to_user;comment.score;migration_info.on_date;migration_info.other_site;migration_info.question_id;question.answers;question.comments;related_site.name;related_site.relation;related_site.site_url;shallow_user.display_name;shallow_user.link;shallow_user.profile_image;shallow_user.reputation;shallow_user.user_id;shallow_user.user_type;site.aliases;site.api_site_parameter;site.audience;site.closed_beta_date;site.favicon_url;site.icon_url;site.launch_date;site.logo_url;site.markdown_extensions;site.name;site.open_beta_date;site.related_sites;site.site_state;site.site_type;site.site_url;site.styling;site.twitter_account;styling.link_color;styling.tag_background_color;styling.tag_foreground_color;badge.description;event.excerpt;event.link;inbox_item.body;info.site;network_user.user_type;post.body;post.comments;post.down_vote_count;post.up_vote_count;reputation.link;reputation.title;revision.body;revision.last_body;suggested_edit.body;tag.last_activity_date;tag_wiki.body;tag_wiki.last_body_editor;tag_wiki.last_excerpt_editor;user.about_me;user.answer_count;user.down_vote_count;user.question_count;user.up_vote_count;user.view_count;user_timeline.link

unsafe:

false

And this generates the error Invalid JSON returned. Inspecting this in the Chrome debugger reveals:

If you're wondering where I got the parameters for this uber filter, I used the default filter editor to select/unselect everything I needed, and sniffed out the request using the debugger.

Please let me know if you need me to clarify anything.