What folder view are you using? Try View > Folders > All. If you cannot see the menu bar, use Alt key to show it.

only upon opening does this side menu of inbox, sent, deleted messages, trash, etc. appaears for about a second, then disappears and i cannot find where it went or how to turn it back on.

Make sure the Thunderbird window is Maximized Move your mouse to the left side of the window and watch for it to change to a double headed arrow When it does, left click, hold and drag to the right and see if you can drag the folder pane back into view.

i did that. it weird. every time i open the program it shows up and then seems to retreat to a hidden location. i have tried everything. i restarted the machine. no change. it does the same thing.

Try restarting with add ons disabled and see if it works better. You can do that from the help menu. You can also hold the shift key when opening Thunderbird to go into safe mode.