What computer operating system are you running Premiere Elements 12 on? Assuming Windows 7, 8, or 8.1 64 bit for now....
In the Premiere Elements 12 Expert workspace, click on the Organizer Tab at the bottom to open the Elements Organizer 12.
When in the Elements Organizer 12, go to Edit Menu/Preferences/Media Analysis and turn off all the options you see under that category, especially AutoAnalyzer options.
When AutoAnalyzer options are left on, the feature will split your video clips and "stack them". When and if you want to use the AutoAnalzyer feature, use it on an on demand basis only. Right click the media in Project Assets and select Run AutoAnalzyer.
The originals on the computer hard drive are unaffected by this unwanted happening. But, you cannot reverse what the AutoAnalzyer has done in the project and Elements Organizer. Instances of these "split stacked" media will need to be deleted and re-imported in Project Assets and Elements Organizer or just left as it.
This can happen in Premiere Elements (any version).
Please let us know if you are OK with the above and if it worked for you.
To answer your first question: Windows 8.
I turned off all the options under AutoAnalyzer and re-imported my footage, but the separate clips are still there. Is there anything else I can do?
Thanks for the follow up.
Please give the suggestion another look.
a. deleted all the stacked split clips in the Elements Organizer and in the project.
b. go to Elements Organizer, Edit Menu/Preferences/Media Analysis and double verify that all those options under Media Analzysis are unchecked.
c. Restart the computer.
d. Import one of your videos into a new Premiere Elements project (Expert workspace) with the project's Add Media/Files and Folders.
e. Click on the Organizer tab at the bottom of the Expert worksapce to open the Elements Organizer. You should see copy of your video that you just imported into Premiere Elements. Do you find the video intact or as a stack of split clips?