Your question is old but yet typical enough that I can imagine more users encounter this. Therefore hereby a belated answer.
What some users might find difficult to understand that making a backup in MySQL (or any other database platform for that matter) is only a part of your entire CMS website.
Basically each (e107) CMS installation consists of four main parts:
- Software e.g. Core/Programs/plugins
- Customisations e.g. themes, themed plugin menus
- Supporting files e.g. download files, images to be displayed in news items
- (My)SQL database
So by saving only the database you have covered only a small part of the entire solution.
Especially when moving to a new version it is best to test it out (preferably locally or in a different sub-folder), in such a way you won't damage your 'live' environment. Once you have did it in a separate test environment you can play with it and see what is wrong. Then fiddle around (hint: note what you did so you can repeat it in your live environment!) until satisfied.
If your test environment fails... oh well.. you can remove it and continue with the current version and your live environment wasn't harmed.
If your test environment is satifactory; make a good back up from all four parts I described above. Set the maintenance flag of your environemt to 'on' to prevent visitors to enter your site while in maintenance mode. Then keep your fingers crossed and repeat on your live environment what you did earlier. Then check, double check, test and remove the maintenance flag.
Hope that will help you (and others) in a hands-on approach of migrating to a new(er) version.