Are you using the Sync feature?

Yes I do have sync on, but I do not have Firefox on any other computers, or phones. I am not sure why having sync on would reverse my changes. In any case where it is moving the icons to are not where they were before I restored my browser

Try to turn off sync and test it for a while.

Looks like it was already off for bookmarks, and its still doing it.

If you use Sync then best is to disconnect Sync temporarily during troubleshooting.

This could be a problem with the places.sqlite and favicons.sqlite files in the Firefox profile folder.

• use the "Places Database" -> "Verify Integrity" button on the "Help -> More Troubleshooting Information" (about:support) page

If errors are reported with "Verify Integrity", close and restart Firefox or reboot and retry.

If "Verify Integrity" cannot repair places.sqlite, rename/remove all places.sqlite and favicons.sqlite files in the Firefox profile folder with Firefox closed. Firefox will rebuild places.sqlite and restore the bookmarks from the most recent JSON backup in the bookmarkbackups folder.

• keep a backup copy of places.sqlite in case a new places.sqlite database has to be created
• you lose the history when a new places.sqlite is created

You may have to restore an older bookmarks backup in the bookmarkbackups folder via the Bookmarks Manager (Library).

• Bookmarks -> Show All Bookmarks -> Import & Backup -> Restore
• https://support.mozilla.org/en-US/kb/restore-bookmarks-from-backup-or-move-them

See also:

• https://support.mozilla.org/en-US/kb/fix-bookmarks-and-history-will-not-be-functional
• https://support.mozilla.org/en-US/kb/cant-add-change-or-save-bookmarks

You can use the button on the "Help -> More Troubleshooting Information" (about:support) page to go to the current Firefox profile folder or use the about:profiles page (Root directory).

• Help -> More Troubleshooting Information -> Profile Folder/Directory:
  Windows: Open Folder; Linux: Open Directory; Mac: Show in Finder
• https://support.mozilla.org/en-US/kb/profiles-where-firefox-stores-user-data

I am not sure what if anything I did but when I closed Firefox and reopened it, it installed a update and the bookmarks toolbar seems to be fine now.

The bookmarks are no longer reordering themselves but what I delete pops right back.

Did you press the "Verify Integrity" button? It should output a log. Paste it here for an analysis.

> Task: checkIntegrity + The places.sqlite database is sane + The favicons.sqlite database is sane > Task: invalidateCaches + The caches have been invalidated > Task: checkCoherence + The database is coherent > Task: expire + Database cleaned up > Task: originFrecencyStats + Recalculated origin frecency stats > Task: vacuum + Initial database size is 5120KiB + The database has been vacuumed + Final database size is 5120KiB > Task: stats + Places.sqlite size is 5120KiB + Favicons.sqlite size is 5120KiB + pragma_user_version is 59 + pragma_page_size is 32768 + pragma_cache_size is -2048 + pragma_journal_mode is wal + pragma_synchronous is 1 + History can store a maximum of 112348 unique pages + Table moz_origins has 471 records + Table moz_places has 789 records + Table moz_historyvisits has 368 records + Table moz_inputhistory has 3 records + Table moz_bookmarks has 579 records + Table moz_bookmarks_deleted has 0 records + Table moz_keywords has 0 records + Table sqlite_sequence has 1 records + Table moz_anno_attributes has 0 records + Table moz_annos has 0 records + Table moz_items_annos has 0 records + Table moz_meta has 6 records + Table moz_places_metadata has 0 records + Table moz_places_metadata_search_queries has 0 records + Table moz_places_metadata_snapshots has 0 records + Table moz_places_metadata_snapshots_extra has 0 records + Table moz_places_metadata_snapshots_groups has 0 records + Table moz_places_metadata_groups_to_snapshots has 0 records + Table moz_session_metadata has 0 records + Table moz_session_to_places has 0 records + Table sqlite_stat1 has 13 records + Pages sequentiality: 92.5 + sqlite_schema: 32KiB (1.9%), 27.5% eff. + moz_origins: 32KiB (1.9%), 53.3% eff. + sqlite_autoindex_moz_origins_1: 32KiB (1.9%), 49% eff. + moz_historyvisits: 32KiB (1.9%), 26% eff. + moz_inputhistory: 32KiB (1.9%), 0.2% eff. + sqlite_autoindex_moz_inputhistory_1: 32KiB (1.9%), 0.1% eff. + moz_bookmarks_deleted: 32KiB (1.9%), 0% eff. + sqlite_autoindex_moz_bookmarks_deleted_1: 32KiB (1.9%), 0% eff. + moz_keywords: 32KiB (1.9%), 0% eff. + sqlite_autoindex_moz_keywords_1: 32KiB (1.9%), 0% eff. + sqlite_sequence: 32KiB (1.9%), 0.1% eff. + moz_anno_attributes: 32KiB (1.9%), 0% eff. + sqlite_autoindex_moz_anno_attributes_1: 32KiB (1.9%), 0% eff. + moz_annos: 32KiB (1.9%), 0% eff. + moz_items_annos: 32KiB (1.9%), 0% eff. + moz_meta: 32KiB (1.9%), 0.7% eff. + moz_places_metadata: 32KiB (1.9%), 0% eff. + moz_places_metadata_search_queries: 32KiB (1.9%), 0% eff. + sqlite_autoindex_moz_places_metadata_search_queries_1: 32KiB (1.9%), 0% eff. + moz_places_metadata_snapshots: 32KiB (1.9%), 0% eff. + moz_places_metadata_snapshots_extra: 32KiB (1.9%), 0% eff. + moz_places_metadata_snapshots_groups: 32KiB (1.9%), 0% eff. + moz_places_metadata_groups_to_snapshots: 32KiB (1.9%), 0% eff. + moz_session_metadata: 32KiB (1.9%), 0% eff. + sqlite_autoindex_moz_session_metadata_1: 32KiB (1.9%), 0% eff. + moz_session_to_places: 32KiB (1.9%), 0% eff. + sqlite_stat1: 32KiB (1.9%), 2.1% eff. + moz_places_url_hashindex: 32KiB (1.9%), 33.4% eff. + moz_places_hostindex: 32KiB (1.9%), 61% eff. + moz_places_visitcount: 32KiB (1.9%), 19.1% eff. + moz_places_frecencyindex: 32KiB (1.9%), 23.1% eff. + moz_places_lastvisitdateindex: 32KiB (1.9%), 25.4% eff. + moz_places_guid_uniqueindex: 32KiB (1.9%), 47.8% eff. + moz_places_originidindex: 32KiB (1.9%), 23% eff. + moz_historyvisits_placedateindex: 32KiB (1.9%), 21% eff. + moz_historyvisits_fromindex: 32KiB (1.9%), 10.1% eff. + moz_historyvisits_dateindex: 32KiB (1.9%), 17.6% eff. + moz_bookmarks_itemindex: 32KiB (1.9%), 18.6% eff. + moz_bookmarks_parentindex: 32KiB (1.9%), 19.7% eff. + moz_bookmarks_itemlastmodifiedindex: 32KiB (1.9%), 32.6% eff. + moz_bookmarks_dateaddedindex: 32KiB (1.9%), 27.9% eff. + moz_bookmarks_guid_uniqueindex: 32KiB (1.9%), 35% eff. + moz_keywords_placepostdata_uniqueindex: 32KiB (1.9%), 0% eff. + moz_annos_placeattributeindex: 32KiB (1.9%), 0% eff. + moz_items_annos_itemattributeindex: 32KiB (1.9%), 0% eff. + moz_places_metadata_placecreated_uniqueindex: 32KiB (1.9%), 0% eff. + moz_bookmarks: 96KiB (5.6%), 50.1% eff. + moz_places: 160KiB (9.3%), 77.7% eff. > Task: _refreshUI

Currently it seems to be putting the bookmarks in alphabetical order despite the fact that I never told it to do that.