Actually, after looking at several responses via Google searches and spending hours looking at my problem with imported bookmarks creating one folder per website I had in my bookmarks, it appears I finally fixed the problem. Here's what I did to fix it. Hope it works for you as well and saves you some time looking for a solution.
I am using Windows 7 OS. Please note that these steps will delete ALL Google Chrome bookmarks from your browser. Then, you will import from IE (or whatever browser you choose) so you have a clean copy without duplicate bookmarks being shown in Chrome. Please note the steps are easy. I just broke them down to be very specific and clear in several steps for better results.
If you have more than one computer with this problem, then do these steps on all computers at the same time. Otherwise, bookmarks on one computer will mess up the others when you Sign in to Chrome (and you'll have duplicates again).
1) Go to the Chrome menu, using the icon in the upper right corner, and select Settings. In the Sign In section, click on the "Google Dashboard" link.
2) On the Google Dashboard screen, press the "Stop and Clear" button, then confirm by selecting "OK" on the next window.
3) After the Google Dashboard clear is complete, on the Settings screen, press the "Disconnect your Google Account..." button. Then, confirm with "Disconnect account" on the next window.
4) Exit out of ALL Chrome browser windows.
5) Go to your C: Drive and search for "Bookmarks" in the Search field.
6) Right click on the result that says "C:\Users\username\AppData\Local\Google\Chrome\User Data\Default" and select the "Open File Location" menu item.
7) Delete the Bookmarks and Bookmarks.bak files.
8) Open a Chrome browser window. You will notice there are no bookmarks, but there is a link at the top stating that you can Import your bookmarks. Click on that link and follow the prompts to import from whatever browser window you choose. Your bookmarks will be shown once they have all been imported.
9) On the Settings screen, press the "Sign in to Chrome" button, then enter your Google email and password. Then, confirm with "OK, sync everything" on the next window.
10) There you go... Now the bookmarks should be correct and they are now uploaded to your Google Account for easy syncing to other computers. You may want to turn off syncing temporarily or permanently to preserve your bookmark list.
Enjoy your day. I know I will now that I finally figured this out!