There must be a simple program to do this sort of task, but I'm afraid I don't know any myself.
To remove manually the dead unticked entries in msconfig startup tab, note down the locations in the registry first (such as HKLM\Software\...\Run), retick them [this is the silly part], click OK to exit msconfig, then immediately open regedit, navigate to the relevant key, and delete the items on the right.
The startup items in the registry shown in msconfig are usually found in HKEY Local Machine (or HKEY Current User)\ Software\ Microsoft\ Windows\ Current Version\ Run
Highlight Run on the left, find the items on the right, right click the name, delete, confirm.
After the deletions, the items should not appear in msconfig any more.