Is one of the packages you installed SideBarEnhancements?
If it is then that could produce the issues you are reporting.
If that's a possibility check the github page for SideBarEnhancements https://github.com/titoBouzout/SideBarEnhancements
for a discussion of the issue.
When you say you added the packages to ST3 did you copy the files from your ST2 folder structure to the ST3 folder structure or did you add them through Package Control from scratch?
What build of ST3 are you running?
What OS are you running on?